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Nickel in PDB 2bdg: Human Kallikrein 4 Complex with Nickel and P-Aminobenzamidine

Protein crystallography data

The structure of Human Kallikrein 4 Complex with Nickel and P-Aminobenzamidine, PDB code: 2bdg was solved by M.Debela, W.Bode, P.Goettig, Structural Proteomics In Europe (Spine), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.92 / 1.95
Space group P 4
Cell size a, b, c (Å), α, β, γ (°) 95.680, 95.680, 38.800, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 22.5

Nickel Binding Sites:

The binding sites of Nickel atom in the Human Kallikrein 4 Complex with Nickel and P-Aminobenzamidine (pdb code 2bdg). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Human Kallikrein 4 Complex with Nickel and P-Aminobenzamidine, PDB code: 2bdg:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 2bdg

Go back to Nickel Binding Sites List in 2bdg
Nickel binding site 1 out of 4 in the Human Kallikrein 4 Complex with Nickel and P-Aminobenzamidine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Human Kallikrein 4 Complex with Nickel and P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni405

b:27.5
occ:1.00
O A:HOH480 1.9 24.5 1.0
O A:HOH563 2.0 32.2 1.0
OE2 A:GLU77 2.1 27.4 1.0
O A:HOH483 2.1 31.7 1.0
NE2 A:HIS25 2.2 18.3 1.0
O A:HOH486 2.2 28.6 1.0
CE1 A:HIS25 3.0 15.1 1.0
CD A:GLU77 3.0 25.9 1.0
O A:HOH557 3.1 49.3 1.0
OE1 A:GLU77 3.3 27.5 1.0
CD2 A:HIS25 3.3 17.1 1.0
ND1 A:HIS25 4.1 16.0 1.0
CG A:HIS25 4.3 17.9 1.0
CG A:GLU77 4.4 28.3 1.0
O A:GLN76 4.7 22.7 1.0
CB A:PRO24 4.8 20.5 1.0
CB A:GLU77 4.8 25.0 1.0
CA A:GLU77 4.9 24.6 1.0

Nickel binding site 2 out of 4 in 2bdg

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Nickel binding site 2 out of 4 in the Human Kallikrein 4 Complex with Nickel and P-Aminobenzamidine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Human Kallikrein 4 Complex with Nickel and P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni408

b:49.4
occ:1.00
O A:HOH556 2.3 25.6 1.0
O A:HOH550 2.6 48.9 1.0
O A:HOH558 2.6 46.2 1.0
O A:HOH560 2.7 52.8 1.0
O A:ASN37 3.5 58.0 1.0
OE1 A:GLU74 4.1 28.0 1.0
C A:ASN37 4.5 55.6 1.0
O A:HOH432 4.6 13.7 1.0
O A:GLU36 4.6 53.4 1.0
O A:HOH518 4.7 39.9 1.0
CA A:ASN37 4.8 55.0 1.0

Nickel binding site 3 out of 4 in 2bdg

Go back to Nickel Binding Sites List in 2bdg
Nickel binding site 3 out of 4 in the Human Kallikrein 4 Complex with Nickel and P-Aminobenzamidine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Human Kallikrein 4 Complex with Nickel and P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni406

b:25.0
occ:1.00
O B:HOH537 2.0 23.3 1.0
O B:HOH536 2.1 27.9 1.0
NE2 B:HIS25 2.1 17.0 1.0
OE1 B:GLU77 2.1 25.6 1.0
O B:HOH535 2.1 22.1 1.0
O B:HOH534 2.1 25.6 1.0
CD2 B:HIS25 3.1 17.6 1.0
CD B:GLU77 3.1 20.4 1.0
CE1 B:HIS25 3.1 14.7 1.0
OE2 B:GLU77 3.3 22.3 1.0
O B:HOH542 3.4 46.5 1.0
O B:HOH529 3.8 33.5 1.0
ND1 B:HIS25 4.2 15.7 1.0
CG B:HIS25 4.2 17.2 1.0
CG B:GLU77 4.5 23.6 1.0
CB B:PRO24 4.5 17.3 1.0
CB B:GLU77 4.8 22.4 1.0
CD B:PRO78 4.9 25.6 1.0
CA B:GLU77 4.9 22.9 1.0

Nickel binding site 4 out of 4 in 2bdg

Go back to Nickel Binding Sites List in 2bdg
Nickel binding site 4 out of 4 in the Human Kallikrein 4 Complex with Nickel and P-Aminobenzamidine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Human Kallikrein 4 Complex with Nickel and P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni407

b:70.5
occ:1.00
O B:HOH540 2.0 36.8 1.0
O B:HOH538 2.2 34.6 1.0
O B:HOH539 2.8 49.3 1.0
OE1 B:GLU36 2.8 62.5 0.0
OG1 B:THR64 3.6 26.0 1.0
CD B:GLU36 3.8 61.6 0.0
CG B:GLU36 4.1 60.4 0.0
OE2 B:GLU84 4.4 30.5 1.0
N B:GLU36 4.8 54.6 1.0
CB B:THR64 4.8 23.0 1.0
OE2 B:GLU36 4.9 62.5 0.0
OE1 B:GLU84 4.9 29.5 1.0

Reference:

M.Debela, V.Magdolen, V.Grimminger, C.Sommerhoff, A.Messerschmidt, R.Huber, R.Friedrich, W.Bode, P.Goettig. Crystal Structures of Human Tissue Kallikrein 4: Activity Modulation By A Specific Zinc Binding Site. J.Mol.Biol. V. 362 1094 2006.
ISSN: ISSN 0022-2836
PubMed: 16950394
DOI: 10.1016/J.JMB.2006.08.003
Page generated: Fri Sep 25 08:06:22 2020
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