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Nickel in PDB 2jk8: Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety

Protein crystallography data

The structure of Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety, PDB code: 2jk8 was solved by D.V.Palanivelu, T.Schirmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.948, 82.877, 126.729, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 27.5

Other elements in 2jk8:

The structure of Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety (pdb code 2jk8). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety, PDB code: 2jk8:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 2jk8

Go back to Nickel Binding Sites List in 2jk8
Nickel binding site 1 out of 4 in the Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni501

b:68.2
occ:1.00
O A:HOH2001 1.9 57.1 1.0
NE2 A:HIS18 2.0 64.4 1.0
NE2 A:HIS17 2.1 72.2 1.0
O A:HOH2002 2.8 53.7 1.0
CE1 A:HIS17 2.8 70.3 1.0
CE1 A:HIS18 2.9 62.9 1.0
CD2 A:HIS18 3.1 61.6 1.0
CD2 A:HIS17 3.2 71.2 1.0
ND1 A:HIS17 4.0 68.9 1.0
O A:GLU12 4.0 74.9 1.0
ND1 A:HIS18 4.0 59.0 1.0
CG A:HIS18 4.1 59.4 1.0
CG A:HIS17 4.2 66.2 1.0
CB A:SER15 4.8 60.6 1.0

Nickel binding site 2 out of 4 in 2jk8

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Nickel binding site 2 out of 4 in the Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni502

b:60.0
occ:1.00
NZ A:LYS49 2.0 53.9 1.0
NE2 B:HIS231 2.0 56.7 1.0
NE2 A:HIS45 2.1 65.8 1.0
O B:HOH2003 2.1 35.8 1.0
O A:HOH2003 2.4 41.8 1.0
CE1 A:HIS45 2.8 62.5 1.0
CE A:LYS49 2.8 56.1 1.0
CE1 B:HIS231 2.9 54.5 1.0
CD2 B:HIS231 3.1 59.0 1.0
CD2 A:HIS45 3.3 63.6 1.0
ND1 B:HIS231 4.0 51.1 1.0
ND1 A:HIS45 4.0 56.0 1.0
CG B:HIS231 4.1 55.9 1.0
CD A:LYS49 4.3 57.1 1.0
CG A:HIS45 4.3 57.7 1.0

Nickel binding site 3 out of 4 in 2jk8

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Nickel binding site 3 out of 4 in the Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni501

b:75.3
occ:1.00
NE2 B:HIS17 2.0 71.7 1.0
NE2 B:HIS18 2.1 65.8 1.0
O B:HOH2002 2.2 57.2 1.0
CE1 B:HIS17 2.4 70.8 1.0
CE1 B:HIS18 2.9 62.2 1.0
CD2 B:HIS18 3.0 60.9 1.0
CD2 B:HIS17 3.3 69.9 1.0
O B:HOH2001 3.3 53.0 1.0
ND1 B:HIS17 3.6 69.0 1.0
ND1 B:HIS18 4.0 59.6 1.0
CG B:HIS18 4.1 58.0 1.0
CG B:HIS17 4.1 65.3 1.0
O B:GLU12 4.1 71.5 1.0
CB B:SER15 4.8 61.7 1.0

Nickel binding site 4 out of 4 in 2jk8

Go back to Nickel Binding Sites List in 2jk8
Nickel binding site 4 out of 4 in the Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni502

b:64.6
occ:1.00
NZ B:LYS49 2.0 55.3 1.0
NE2 A:HIS231 2.0 57.7 1.0
NE2 B:HIS45 2.1 65.2 1.0
O A:HOH2004 2.1 38.5 1.0
CE1 A:HIS231 2.7 54.8 1.0
CE B:LYS49 2.7 57.2 1.0
CE1 B:HIS45 2.9 62.8 1.0
CD2 A:HIS231 3.1 58.9 1.0
CD2 B:HIS45 3.1 63.3 1.0
ND1 A:HIS231 3.9 51.5 1.0
CG A:HIS231 4.1 56.1 1.0
ND1 B:HIS45 4.1 58.3 1.0
CD B:LYS49 4.2 57.6 1.0
CG B:HIS45 4.2 58.9 1.0
OD2 B:ASP46 4.5 66.5 1.0

Reference:

D.V.Palanivelu, A.Goepfert, M.Meury, P.Guye, C.Dehio, T.Schirmer. Fic Domain Catalyzed Adenylylation: Insight Provided By the Structural Analysis of the Type IV Secretion System Effector Bepa. Protein Sci. V. 20 492 2011.
ISSN: ISSN 0961-8368
PubMed: 21213248
DOI: 10.1002/PRO.581
Page generated: Thu Oct 29 06:17:35 2020
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