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Nickel in PDB 2v4b: Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form)

Protein crystallography data

The structure of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form), PDB code: 2v4b was solved by S.Gerhardt, G.Hassall, P.Hawtin, E.Mccall, L.Flavell, C.Minshull, D.Hargreaves, A.Ting, R.A.Pauptit, A.E.Parker, W.M.Abbott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.26 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.579, 64.396, 113.524, 90.00, 90.91, 90.00
R / Rfree (%) 22 / 26.3

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form) (pdb code 2v4b). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 14 binding sites of Nickel where determined in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form), PDB code: 2v4b:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13; 14;

Nickel binding site 1 out of 14 in 2v4b

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Nickel binding site 1 out of 14 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form)


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Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1555

b:40.2
occ:1.00
NE2 B:HIS313 2.2 47.1 1.0
O B:HOH2007 2.3 45.0 1.0
OE1 A:GLU494 2.5 48.3 1.0
O A:HOH2106 2.5 37.2 1.0
O B:HOH2003 2.6 48.4 1.0
OE2 A:GLU494 2.6 49.0 1.0
CD A:GLU494 2.9 46.1 1.0
CD2 B:HIS313 2.9 46.4 1.0
CE1 B:HIS313 3.4 47.5 1.0
O A:HOH2107 4.1 53.8 1.0
CG B:HIS313 4.2 47.5 1.0
ND1 B:HIS313 4.3 47.2 1.0
CG A:GLU494 4.4 43.1 1.0
CB B:ALA271 4.6 39.6 1.0
O B:GLY275 4.7 37.0 1.0
O B:ALA271 4.7 39.2 1.0
C B:GLY275 4.9 36.9 1.0

Nickel binding site 2 out of 14 in 2v4b

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Nickel binding site 2 out of 14 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form)


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Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1556

b:26.0
occ:1.00
O B:HOH2057 1.8 48.3 1.0
O A:HOH2013 2.1 34.7 1.0
OD1 B:ASP483 2.1 36.3 1.0
ND1 A:HIS280 2.2 27.8 1.0
CE1 A:HIS280 3.0 30.8 1.0
CG B:ASP483 3.1 35.4 1.0
CG A:HIS280 3.3 30.3 1.0
OD2 B:ASP483 3.3 35.4 1.0
CB A:HIS280 3.7 27.9 1.0
O B:HOH2056 4.2 46.0 1.0
NE2 A:HIS280 4.2 33.4 1.0
CA A:HIS280 4.3 28.0 1.0
CD2 A:HIS280 4.3 31.7 1.0
CG B:ARG486 4.4 31.2 1.0
CB B:ASP483 4.5 33.5 1.0
ND2 B:ASN485 4.5 35.5 1.0
CB B:ASN485 4.5 31.8 1.0
CD B:ARG486 4.8 33.2 1.0

Nickel binding site 3 out of 14 in 2v4b

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Nickel binding site 3 out of 14 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form)


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Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1557

b:28.2
occ:1.00
O A:HOH2089 2.2 33.9 1.0
OE1 A:GLU261 2.3 31.6 1.0
OD1 A:ASP465 2.4 39.5 1.0
O A:CYS462 2.4 32.7 1.0
OD2 A:ASP351 2.6 34.3 1.0
OD1 A:ASP351 2.6 31.4 1.0
OD2 A:ASP344 2.6 50.6 1.0
CG A:ASP351 3.0 31.8 1.0
CD A:GLU261 3.3 34.2 1.0
CG A:ASP344 3.4 49.9 1.0
OD1 A:ASP344 3.4 48.4 1.0
CG A:ASP465 3.4 36.9 1.0
C A:CYS462 3.6 33.1 1.0
OD2 A:ASP465 3.7 34.1 1.0
CD A:CD1553 4.0 38.0 1.0
CG A:GLU261 4.0 32.4 1.0
CA A:LEU463 4.3 33.1 1.0
OE2 A:GLU261 4.3 38.3 1.0
O A:TYR259 4.3 34.5 1.0
N A:LEU463 4.3 33.0 1.0
CB A:GLU261 4.4 32.6 1.0
CB A:ASP351 4.4 31.7 1.0
O A:ASP465 4.5 37.2 1.0
CA A:CYS462 4.6 33.2 1.0
CB A:CYS462 4.6 33.5 1.0
O A:HOH2047 4.7 35.9 1.0
O A:HOH2087 4.7 44.0 1.0
C A:LEU463 4.8 33.5 1.0
CB A:ASP465 4.8 36.5 1.0
N A:ASP465 4.9 35.9 1.0
CB A:ASP344 4.9 49.0 1.0

Nickel binding site 4 out of 14 in 2v4b

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Nickel binding site 4 out of 14 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form)


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Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1558

b:37.8
occ:1.00
O A:HOH2009 2.4 43.0 1.0
O A:HOH2006 2.4 46.1 1.0
NE2 A:HIS313 2.4 36.8 1.0
O A:HOH2024 2.5 36.1 1.0
CD2 A:HIS313 3.1 36.4 1.0
OE2 B:GLU494 3.5 50.2 1.0
CE1 A:HIS313 3.6 34.9 1.0
CD B:GLU494 3.7 46.5 1.0
OE1 B:GLU494 4.1 49.0 1.0
CG B:GLU494 4.2 43.5 1.0
O B:HOH2062 4.3 39.4 1.0
CG A:HIS313 4.3 35.6 1.0
O B:HOH2004 4.3 47.7 1.0
O A:GLY275 4.4 34.7 1.0
ND1 A:HIS313 4.5 37.1 1.0
O A:ALA271 4.6 35.5 1.0
CB A:ALA271 4.6 34.6 1.0
C A:GLY275 4.7 33.9 1.0
CB B:GLU494 4.9 41.2 1.0
CA A:GLY275 4.9 33.9 1.0

Nickel binding site 5 out of 14 in 2v4b

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Nickel binding site 5 out of 14 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form)


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Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1559

b:59.6
occ:1.00
OE2 A:GLU320 2.3 37.3 1.0
O A:HOH2027 3.1 35.4 1.0
CD A:GLU320 3.2 37.5 1.0
OE1 A:GLU320 3.3 39.6 1.0
CD A:CD1554 3.8 35.4 1.0
OE1 A:GLU315 4.5 34.0 1.0
CG A:GLU320 4.6 34.5 1.0
O A:HOH2031 4.7 28.9 1.0

Nickel binding site 6 out of 14 in 2v4b

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Nickel binding site 6 out of 14 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form)


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Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1561

b:34.3
occ:1.00
O A:HOH2075 1.9 22.5 1.0
NE2 A:HIS428 2.3 39.3 1.0
CE1 A:HIS428 3.2 39.0 1.0
CD2 A:HIS428 3.3 39.3 1.0
ND1 A:HIS428 4.3 38.7 1.0
CG A:HIS428 4.4 38.3 1.0
OG A:SER427 4.5 40.1 1.0
CD A:PRO445 4.6 36.7 1.0

Nickel binding site 7 out of 14 in 2v4b

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Nickel binding site 7 out of 14 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1562

b:53.0
occ:1.00
OD1 A:ASP495 2.7 41.9 1.0
OE2 A:GLU494 3.0 49.0 1.0
CE1 B:HIS313 3.4 47.5 1.0
CG A:ASP495 3.7 41.2 1.0
CD A:GLU494 3.8 46.1 1.0
CG A:GLU494 3.8 43.1 1.0
OD2 A:ASP495 4.0 43.7 1.0
NZ B:LYS279 4.1 39.2 1.0
ND1 B:HIS313 4.2 47.2 1.0
NE2 B:HIS313 4.3 47.1 1.0
O A:HOH2107 4.7 53.8 1.0
CE B:LYS279 4.8 36.3 1.0
N A:ASP495 4.9 38.9 1.0
CB A:ASP495 4.9 39.3 1.0
OE1 A:GLU494 5.0 48.3 1.0

Nickel binding site 8 out of 14 in 2v4b

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Nickel binding site 8 out of 14 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form)


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Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1563

b:48.7
occ:1.00
ND1 A:HIS498 2.4 39.9 1.0
O A:HOH2109 2.8 42.5 1.0
CE1 A:HIS498 3.2 41.7 1.0
CG A:HIS498 3.5 38.5 1.0
CB A:HIS498 3.9 37.7 1.0
CG A:PRO500 4.2 43.0 1.0
O A:HOH2100 4.3 39.9 1.0
NE2 A:HIS498 4.4 41.9 1.0
CD2 A:HIS498 4.5 41.0 1.0
CB A:ALA484 4.5 31.6 1.0
OD1 A:ASN485 4.8 31.3 1.0
CB A:PRO500 4.9 43.6 1.0
O A:HOH2099 5.0 30.7 1.0

Nickel binding site 9 out of 14 in 2v4b

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Nickel binding site 9 out of 14 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form)


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Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1564

b:68.0
occ:1.00
NE2 A:HIS525 2.5 43.5 1.0
CD2 A:HIS525 3.3 43.0 1.0
CE1 A:HIS525 3.7 43.9 1.0
O A:THR523 4.3 35.6 1.0
CG A:HIS525 4.5 41.1 1.0
ND1 A:HIS525 4.7 43.8 1.0

Nickel binding site 10 out of 14 in 2v4b

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Nickel binding site 10 out of 14 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1555

b:49.8
occ:1.00
O A:HOH2012 2.2 48.2 1.0
OE2 B:GLU494 2.6 50.2 1.0
OD1 B:ASP495 2.8 42.1 1.0
OE1 B:GLU494 2.9 49.0 1.0
CD B:GLU494 3.0 46.5 1.0
CE1 A:HIS313 3.1 34.9 1.0
CG B:ASP495 3.7 42.3 1.0
O B:HOH2063 3.8 57.5 1.0
ND1 A:HIS313 3.9 37.1 1.0
OD2 B:ASP495 4.0 44.6 1.0
NZ A:LYS279 4.0 43.4 1.0
NE2 A:HIS313 4.1 36.8 1.0
O A:HOH2023 4.3 50.2 1.0
CG B:GLU494 4.4 43.5 1.0
O B:HOH2062 4.7 39.4 1.0
CE A:LYS279 4.8 40.7 1.0
CB A:VAL311 4.8 33.4 1.0
CB B:ASP495 5.0 40.0 1.0

Nickel binding site 11 out of 14 in 2v4b

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Nickel binding site 11 out of 14 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form)


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Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 11 of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1557

b:29.4
occ:1.00
O B:CYS462 2.2 35.9 1.0
OD1 B:ASP465 2.3 42.1 1.0
OD2 B:ASP351 2.3 39.0 1.0
O B:HOH2046 2.3 22.6 1.0
OE1 B:GLU261 2.5 37.1 1.0
OD1 B:ASP351 2.6 38.5 1.0
OD2 B:ASP344 2.6 45.9 1.0
CG B:ASP351 2.8 39.0 1.0
CG B:ASP465 3.3 41.3 1.0
CD B:GLU261 3.4 36.4 1.0
C B:CYS462 3.4 36.2 1.0
CG B:ASP344 3.6 46.9 1.0
OD2 B:ASP465 3.7 40.3 1.0
OD1 B:ASP344 3.8 41.3 1.0
CG B:GLU261 3.9 35.6 1.0
CD B:CD1556 4.0 41.5 1.0
CA B:LEU463 4.2 36.4 1.0
N B:LEU463 4.3 36.0 1.0
O B:TYR259 4.3 35.5 1.0
CB B:GLU261 4.3 34.7 1.0
CB B:ASP351 4.3 38.5 1.0
OE2 B:GLU261 4.3 37.6 1.0
O B:ASP465 4.4 41.6 1.0
CA B:CYS462 4.4 36.4 1.0
CB B:CYS462 4.6 36.4 1.0
CB B:ASP465 4.7 41.1 1.0
C B:LEU463 4.7 37.1 1.0
N B:ASP465 4.8 40.2 1.0
N B:GLU261 5.0 34.8 1.0
CB B:ASP344 5.0 48.0 1.0
SG B:CYS462 5.0 38.0 1.0
N B:MET464 5.0 38.1 1.0

Nickel binding site 12 out of 14 in 2v4b

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Nickel binding site 12 out of 14 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 12 of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1559

b:30.9
occ:1.00
O B:HOH2036 2.3 19.3 1.0
NE2 B:HIS428 2.3 36.5 1.0
CE1 B:HIS428 3.2 34.9 1.0
CD2 B:HIS428 3.3 35.4 1.0
OE1 B:GLN441 4.3 48.6 1.0
ND1 B:HIS428 4.4 33.9 1.0
CG B:HIS428 4.4 35.0 1.0
CD B:PRO445 4.6 32.8 1.0
OG B:SER427 4.9 38.3 1.0

Nickel binding site 13 out of 14 in 2v4b

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Nickel binding site 13 out of 14 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 13 of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1560

b:64.6
occ:1.00
NE2 B:HIS459 2.4 34.2 1.0
O B:HOH2045 3.1 29.6 1.0
CD2 B:HIS459 3.4 34.5 1.0
CE1 B:HIS459 3.4 34.0 1.0
CB B:ASN457 4.2 31.2 1.0
OD1 B:ASN457 4.3 33.6 1.0
ND1 B:HIS459 4.5 34.7 1.0
CG B:ASN457 4.5 32.1 1.0
CG B:HIS459 4.5 34.6 1.0

Nickel binding site 14 out of 14 in 2v4b

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Nickel binding site 14 out of 14 in the Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 14 of Crystal Structure of Human Adamts-1 Catalytic Domain and Cysteine- Rich Domain (Apo-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1561

b:45.0
occ:1.00
ND1 B:HIS498 2.3 40.2 1.0
O B:HOH2064 2.6 46.4 1.0
CE1 B:HIS498 3.1 40.7 1.0
CG B:HIS498 3.4 38.4 1.0
CB B:HIS498 3.8 37.9 1.0
O B:HOH2058 3.8 41.6 1.0
NE2 B:HIS498 4.3 39.3 1.0
CD2 B:HIS498 4.4 38.3 1.0
CB B:ALA484 4.5 31.3 1.0
OD1 B:ASN485 5.0 36.0 1.0
O B:HOH2076 5.0 27.3 1.0

Reference:

S.Gerhardt, G.Hassall, P.Hawtin, E.Mccall, L.Flavell, C.Minshull, D.Hargreaves, A.Ting, R.A.Pauptit, A.E.Parker, W.M.Abbott. Crystal Structures of Human Adamts-1 Reveal A Conserved Catalytic Domain and A Disintegrin-Like Domain with A Fold Homologous to Cysteine-Rich Domains. J.Mol.Biol. V. 373 891 2007.
ISSN: ISSN 0022-2836
PubMed: 17897672
DOI: 10.1016/J.JMB.2007.07.047
Page generated: Fri Sep 25 08:15:16 2020
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