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Zinc in PDB 4dxb: 2.29A Structure of the Engineered Mbp Tem-1 Fusion Protein RG13 in Complex with Zinc, P1 Space Group

Enzymatic activity of 2.29A Structure of the Engineered Mbp Tem-1 Fusion Protein RG13 in Complex with Zinc, P1 Space Group

All present enzymatic activity of 2.29A Structure of the Engineered Mbp Tem-1 Fusion Protein RG13 in Complex with Zinc, P1 Space Group:
3.5.2.6;

Protein crystallography data

The structure of 2.29A Structure of the Engineered Mbp Tem-1 Fusion Protein RG13 in Complex with Zinc, P1 Space Group, PDB code: 4dxb was solved by F.Van Den Akker, W.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.45 / 2.29
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.316, 74.177, 103.130, 83.54, 77.64, 89.98
R / Rfree (%) 23.2 / 29.2

Zinc Binding Sites:

The binding sites of Zinc atom in the 2.29A Structure of the Engineered Mbp Tem-1 Fusion Protein RG13 in Complex with Zinc, P1 Space Group (pdb code 4dxb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the 2.29A Structure of the Engineered Mbp Tem-1 Fusion Protein RG13 in Complex with Zinc, P1 Space Group, PDB code: 4dxb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4dxb

Go back to Zinc Binding Sites List in 4dxb
Zinc binding site 1 out of 4 in the 2.29A Structure of the Engineered Mbp Tem-1 Fusion Protein RG13 in Complex with Zinc, P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 2.29A Structure of the Engineered Mbp Tem-1 Fusion Protein RG13 in Complex with Zinc, P1 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:38.0
occ:1.00
 NE2 A:HIS468 2.1 22.7 1.0
OD1 A:ASP164 2.2 31.5 1.0
O A:HOH861 2.6 31.2 1.0
CG A:ASP164 2.9 29.9 1.0
OD2 A:ASP164 2.9 32.9 1.0
CD2 A:HIS468 3.0 21.2 1.0
CE1 A:HIS468 3.2 23.8 1.0
NE2 A:GLN253 3.7 34.2 1.0
O A:ASP164 4.0 31.4 1.0
NZ A:LYS251 4.1 26.5 1.0
CG A:HIS468 4.2 22.8 1.0
CD A:LYS251 4.2 22.9 1.0
ND1 A:HIS468 4.2 21.5 1.0
CB A:ASP164 4.3 29.8 1.0
OE2 A:GLU477 4.4 29.3 1.0
CD A:GLN253 4.6 34.7 1.0
OD2 A:ASP471 4.6 38.3 1.0
OE1 A:GLU477 4.6 28.0 1.0
OE1 A:GLN253 4.7 35.9 1.0
CD A:GLU477 4.7 26.8 1.0
CE A:LYS251 4.8 24.3 1.0
C A:ASP164 4.8 28.5 1.0
CA A:ASP164 4.8 29.4 1.0
CB A:LYS251 4.9 15.3 1.0

Zinc binding site 2 out of 4 in 4dxb

Go back to Zinc Binding Sites List in 4dxb
Zinc binding site 2 out of 4 in the 2.29A Structure of the Engineered Mbp Tem-1 Fusion Protein RG13 in Complex with Zinc, P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 2.29A Structure of the Engineered Mbp Tem-1 Fusion Protein RG13 in Complex with Zinc, P1 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:24.1
occ:1.00
 ND1 A:HIS514 2.0 18.2 1.0
ND1 A:HIS509 2.1 19.8 1.0
CE1 A:HIS514 3.0 19.9 1.0
CE1 A:HIS509 3.0 20.5 1.0
CG A:HIS509 3.0 20.9 1.0
CG A:HIS514 3.1 20.6 1.0
CB A:HIS509 3.4 21.3 1.0
CB A:HIS514 3.4 21.4 1.0
CA A:HIS514 3.9 22.5 1.0
NE2 A:HIS509 4.1 20.9 1.0
NE2 A:HIS514 4.1 20.7 1.0
CD2 A:HIS509 4.1 22.5 1.0
CD2 A:HIS514 4.1 19.5 1.0
CA A:HIS509 4.3 19.3 1.0
O A:HIS509 4.6 23.6 1.0
C A:HIS509 4.8 22.0 1.0
N A:HIS514 4.8 23.7 1.0
O A:ASP513 4.9 23.9 1.0
C A:HIS514 5.0 22.1 1.0
O A:HIS514 5.0 23.6 1.0

Zinc binding site 3 out of 4 in 4dxb

Go back to Zinc Binding Sites List in 4dxb
Zinc binding site 3 out of 4 in the 2.29A Structure of the Engineered Mbp Tem-1 Fusion Protein RG13 in Complex with Zinc, P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 2.29A Structure of the Engineered Mbp Tem-1 Fusion Protein RG13 in Complex with Zinc, P1 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:36.5
occ:1.00
 NE2 B:HIS468 2.1 20.2 1.0
OD1 B:ASP164 2.4 34.0 1.0
OD2 B:ASP164 2.6 35.8 1.0
CG B:ASP164 2.8 34.7 1.0
O B:HOH803 2.8 24.5 1.0
CD2 B:HIS468 2.9 19.4 1.0
CE1 B:HIS468 3.2 19.6 1.0
NZ B:LYS251 4.0 26.8 1.0
CE B:LYS251 4.0 23.1 1.0
O B:ASP164 4.1 33.1 1.0
CG B:HIS468 4.1 18.3 1.0
ND1 B:HIS468 4.2 19.1 1.0
CB B:ASP164 4.3 33.1 1.0
OD2 B:ASP471 4.3 32.9 1.0
CD B:LYS251 4.5 22.2 1.0
OE2 B:GLU477 4.6 35.4 1.0
CD B:GLU477 4.8 30.7 1.0
OE1 B:GLU477 4.9 32.7 1.0
CB B:LYS251 4.9 18.9 1.0
CA B:ASP164 4.9 32.6 1.0
C B:ASP164 4.9 32.5 1.0

Zinc binding site 4 out of 4 in 4dxb

Go back to Zinc Binding Sites List in 4dxb
Zinc binding site 4 out of 4 in the 2.29A Structure of the Engineered Mbp Tem-1 Fusion Protein RG13 in Complex with Zinc, P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 2.29A Structure of the Engineered Mbp Tem-1 Fusion Protein RG13 in Complex with Zinc, P1 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:27.8
occ:1.00
 NE2 B:HIS39 1.9 30.7 1.0
OH B:TYR17 2.0 25.2 1.0
CZ B:TYR17 2.6 26.1 1.0
CD2 B:HIS39 2.9 32.0 1.0
CE1 B:HIS39 3.0 31.5 1.0
CE1 B:TYR17 3.2 25.7 1.0
CE2 B:TYR17 3.6 25.4 1.0
O B:HOH948 3.9 39.2 1.0
CG B:HIS39 4.0 33.1 1.0
ND1 B:HIS39 4.0 32.1 1.0
CD1 B:TYR17 4.3 26.4 1.0
CD2 B:TYR17 4.6 28.0 1.0
CG B:TYR17 5.0 28.2 1.0

Reference:

W.Ke, A.H.Laurent, M.D.Armstrong, Y.Chen, W.E.Smith, J.Liang, C.M.Wright, M.Ostermeier, F.Van Den Akker. Structure of An Engineered Beta-Lactamase Maltose Binding Protein Fusion Protein: Insights Into Heterotropic Allosteric Regulation. Plos One V. 7 39168 2012.
ISSN: ESSN 1932-6203
PubMed: 22720063
DOI: 10.1371/JOURNAL.PONE.0039168
Page generated: Wed Aug 20 17:14:31 2025

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