Zinc in PDB 7me3: Yfea Oligomer Crystal 3, Form 2

Protein crystallography data

The structure of Yfea Oligomer Crystal 3, Form 2, PDB code: 7me3 was solved by C.D.Radka, S.G.Aller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.45 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.09, 75.85, 106.55, 90, 90, 90
R / Rfree (%) 16.6 / 21.8

Other elements in 7me3:

The structure of Yfea Oligomer Crystal 3, Form 2 also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Manganese (Mn) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Yfea Oligomer Crystal 3, Form 2 (pdb code 7me3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Yfea Oligomer Crystal 3, Form 2, PDB code: 7me3:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 7me3

Go back to Zinc Binding Sites List in 7me3
Zinc binding site 1 out of 3 in the Yfea Oligomer Crystal 3, Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yfea Oligomer Crystal 3, Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:3.7
occ:0.52
MN A:MN402 0.2 4.5 0.1
FE A:FE401 0.5 4.6 0.4
OE1 A:GLU207 1.9 5.8 1.0
OD2 A:ASP282 2.2 10.3 1.0
NE2 A:HIS141 2.3 6.1 1.0
NE2 A:HIS76 2.3 6.3 1.0
OD1 A:ASP282 2.4 6.6 1.0
CD A:GLU207 2.6 8.8 1.0
CG A:ASP282 2.6 8.2 1.0
OE2 A:GLU207 2.7 8.8 1.0
CE1 A:HIS76 3.2 6.3 1.0
CD2 A:HIS141 3.2 5.8 1.0
CE1 A:HIS141 3.2 6.3 1.0
CD2 A:HIS76 3.3 6.9 1.0
O A:HOH546 3.7 14.6 1.0
ND2 A:ASN228 3.9 11.5 1.0
CG A:GLU207 4.1 8.2 1.0
CB A:ASP282 4.1 7.7 1.0
CB A:ALA209 4.2 7.5 1.0
CG A:ASN228 4.3 9.6 1.0
ND1 A:HIS76 4.3 6.6 1.0
ND1 A:HIS141 4.3 6.2 1.0
O A:HOH513 4.3 15.9 1.0
CG A:HIS141 4.3 5.8 1.0
CG A:HIS76 4.4 7.4 1.0
OD1 A:ASN228 4.7 12.4 1.0
CB A:GLU207 4.7 9.2 1.0
CB A:ASN228 4.9 8.2 1.0
CA A:ASP282 5.0 6.2 1.0

Zinc binding site 2 out of 3 in 7me3

Go back to Zinc Binding Sites List in 7me3
Zinc binding site 2 out of 3 in the Yfea Oligomer Crystal 3, Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yfea Oligomer Crystal 3, Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:6.4
occ:0.71
MN B:MN402 0.5 5.2 0.1
FE B:FE401 0.6 4.9 0.2
OE1 B:GLU207 2.0 9.1 1.0
OD2 B:ASP282 2.0 8.8 1.0
NE2 B:HIS141 2.3 6.3 1.0
NE2 B:HIS76 2.3 6.8 1.0
CD B:GLU207 2.5 13.5 1.0
OE2 B:GLU207 2.5 13.1 1.0
OD1 B:ASP282 2.6 8.0 1.0
CG B:ASP282 2.6 9.6 1.0
CE1 B:HIS141 3.2 7.1 1.0
CD2 B:HIS76 3.2 7.2 1.0
CD2 B:HIS141 3.2 5.9 1.0
CE1 B:HIS76 3.2 9.2 1.0
ND2 B:ASN228 3.6 16.5 1.0
O B:HOH514 3.9 10.9 1.0
CG B:GLU207 4.0 9.5 1.0
CB B:ALA209 4.1 7.1 1.0
CB B:ASP282 4.1 6.2 1.0
CG B:ASN228 4.2 16.9 1.0
ND1 B:HIS141 4.3 6.3 1.0
CG B:HIS141 4.3 9.5 1.0
ND1 B:HIS76 4.4 9.0 1.0
CG B:HIS76 4.4 10.1 1.0
O B:HOH518 4.4 14.7 1.0
OD1 B:ASN228 4.7 12.8 1.0
CB B:GLU207 4.8 10.8 1.0
CB B:ASN228 4.9 12.7 1.0

Zinc binding site 3 out of 3 in 7me3

Go back to Zinc Binding Sites List in 7me3
Zinc binding site 3 out of 3 in the Yfea Oligomer Crystal 3, Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yfea Oligomer Crystal 3, Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn405

b:27.1
occ:0.84
MN B:MN404 0.4 27.2 0.2
ND1 B:HIS163 2.3 22.1 1.0
CE1 B:HIS163 3.2 26.4 1.0
CG B:HIS163 3.3 18.3 1.0
CB B:HIS163 3.6 10.2 1.0
CA B:HIS163 4.0 16.0 1.0
CG B:PRO116 4.2 19.5 1.0
NE2 B:HIS163 4.3 19.4 1.0
CD2 B:HIS163 4.4 12.3 1.0
O B:HIS163 4.6 23.2 1.0
C B:HIS163 4.9 14.1 1.0
CB B:PRO116 4.9 16.8 1.0
N B:HIS163 5.0 14.1 1.0

Reference:

C.D.Radka, S.G.Aller. Yersinia Pestis Substrate-Binding Protein Yfea Site 2 Is A Dynamic and Polyspecific Surface Metal Binding Site To Be Published.
Page generated: Fri Sep 24 17:07:25 2021

Last articles

Cd in 3G71
Cd in 3G4S
Cd in 3G6E
Cd in 3FYI
Cd in 3FYE
Cd in 3FQU
Cd in 3FQX
Cd in 3FQW
Cd in 3FQT
Cd in 3FQR
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy