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Zinc in PDB 4fsb: Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A

Protein crystallography data

The structure of Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A, PDB code: 4fsb was solved by K.Herzog, K.M.Hoffmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.06 / 1.88
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 67.020, 80.130, 77.639, 90.00, 91.71, 90.00
R / Rfree (%) 14.7 / 19.5

Other elements in 4fsb:

The structure of Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A (pdb code 4fsb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A, PDB code: 4fsb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4fsb

Go back to Zinc Binding Sites List in 4fsb
Zinc binding site 1 out of 4 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:13.2
occ:1.00
O A:HOH450 1.9 11.2 1.0
ND1 A:HIS114 2.0 11.5 1.0
NE2 A:HIS112 2.1 11.2 1.0
NE2 A:HIS177 2.1 10.7 1.0
O A:HOH413 2.4 15.0 1.0
CE1 A:HIS114 2.9 11.6 1.0
CG A:HIS114 3.0 11.6 1.0
CE1 A:HIS112 3.0 11.2 1.0
CD2 A:HIS177 3.0 10.1 1.0
CD2 A:HIS112 3.1 11.0 1.0
CE1 A:HIS177 3.2 10.7 1.0
CB A:HIS114 3.4 12.2 1.0
OD2 A:OCS196 3.7 13.3 1.0
O A:HOH568 4.0 24.4 1.0
O A:HOH516 4.0 28.7 1.0
NE2 A:HIS114 4.1 11.5 1.0
OD1 A:ASP116 4.1 18.1 1.0
CD2 A:HIS114 4.1 12.0 1.0
ND1 A:HIS112 4.1 11.1 1.0
CG A:HIS112 4.2 11.3 1.0
CG A:HIS177 4.3 10.2 1.0
ND1 A:HIS177 4.3 10.6 1.0
SG A:OCS196 4.6 13.5 1.0
OD3 A:OCS196 4.6 13.3 1.0
CB A:OCS196 4.7 12.1 1.0
CA A:HIS114 4.8 13.4 1.0
ND2 A:ASN208 4.8 52.5 1.0
O A:HOH403 4.9 14.4 1.0
CG A:ASP116 4.9 17.5 1.0
OD2 A:ASP116 4.9 19.1 1.0

Zinc binding site 2 out of 4 in 4fsb

Go back to Zinc Binding Sites List in 4fsb
Zinc binding site 2 out of 4 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:14.9
occ:1.00
O A:HOH642 2.0 10.8 1.0
O A:HOH640 2.1 10.5 1.0
ND1 A:HIS249 2.2 11.2 1.0
O A:HOH641 2.7 18.1 1.0
O A:HOH643 2.9 15.3 1.0
CE1 A:HIS249 3.1 11.0 1.0
CG A:HIS249 3.2 10.6 1.0
CB A:HIS249 3.6 11.0 1.0
CA A:HIS249 3.9 11.1 1.0
O A:HOH644 4.2 29.8 1.0
NE2 A:HIS249 4.2 10.4 1.0
ND2 A:ASN252 4.3 13.3 1.0
CD2 A:HIS249 4.3 10.9 1.0
CD2 A:LEU201 4.6 14.9 1.0
O A:HIS249 4.7 12.0 1.0
C A:HIS249 4.8 10.9 1.0
N A:HIS249 4.9 11.4 1.0
CB A:ASN252 5.0 13.9 1.0
O A:LEU201 5.0 17.6 1.0

Zinc binding site 3 out of 4 in 4fsb

Go back to Zinc Binding Sites List in 4fsb
Zinc binding site 3 out of 4 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:16.3
occ:1.00
O B:HOH620 2.0 12.2 1.0
O B:HOH623 2.1 12.8 1.0
ND1 B:HIS249 2.1 11.6 1.0
O B:HOH624 2.7 26.2 1.0
CE1 B:HIS249 3.0 11.8 1.0
O B:HOH621 3.1 16.6 1.0
CG B:HIS249 3.1 11.6 1.0
CB B:HIS249 3.6 11.5 1.0
CA B:HIS249 3.8 12.6 1.0
NE2 B:HIS249 4.2 11.3 1.0
O B:HOH622 4.2 21.0 1.0
CD2 B:HIS249 4.3 11.0 1.0
ND2 B:ASN252 4.3 15.4 1.0
O B:HIS249 4.6 13.8 1.0
CD2 B:LEU201 4.7 13.5 1.0
C B:HIS249 4.7 12.7 1.0
N B:HIS249 4.9 13.2 1.0
CB B:ASN252 5.0 15.1 1.0

Zinc binding site 4 out of 4 in 4fsb

Go back to Zinc Binding Sites List in 4fsb
Zinc binding site 4 out of 4 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:12.5
occ:1.00
ND1 B:HIS114 2.0 14.5 1.0
O B:HOH448 2.0 11.0 1.0
NE2 B:HIS177 2.1 11.1 1.0
NE2 B:HIS112 2.2 13.1 1.0
O B:HOH407 2.4 12.6 1.0
CE1 B:HIS114 3.0 15.1 1.0
CD2 B:HIS177 3.0 11.2 1.0
CG B:HIS114 3.0 13.9 1.0
CE1 B:HIS112 3.1 13.4 1.0
CE1 B:HIS177 3.1 10.6 1.0
CD2 B:HIS112 3.2 13.4 1.0
CB B:HIS114 3.4 13.2 1.0
OD2 B:OCS196 3.6 14.5 1.0
O B:HOH475 4.0 32.7 1.0
NE2 B:HIS114 4.1 16.3 1.0
OD1 B:ASP116 4.1 16.2 1.0
CD2 B:HIS114 4.2 14.6 1.0
O B:HOH480 4.2 24.4 1.0
CG B:HIS177 4.2 10.7 1.0
ND1 B:HIS177 4.2 11.8 1.0
ND1 B:HIS112 4.2 12.5 1.0
CG B:HIS112 4.3 12.9 1.0
SG B:OCS196 4.6 14.5 1.0
CB B:OCS196 4.6 13.3 1.0
OD3 B:OCS196 4.7 14.0 1.0
CA B:HIS114 4.8 13.1 1.0
O B:HOH425 4.9 15.4 1.0
CG B:ASP116 5.0 15.6 1.0
OD2 B:ASP116 5.0 18.4 1.0

Reference:

M.B.Kupper, K.Herzog, S.Bennink, P.Schlomer, P.Bogaerts, Y.Glupczynski, R.Fischer, C.Bebrone, K.M.Hoffmann. The Three-Dimensional Structure of Vim-31 - A Metallo-Beta-Lactamase From Enterobacter Cloacae in Its Native and Oxidized Form. Febs J. V. 282 2352 2015.
ISSN: ISSN 1742-464X
PubMed: 25825035
DOI: 10.1111/FEBS.13283
Page generated: Wed Dec 16 05:18:05 2020

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