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Manganese 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:

Zinc (Zn) 3 atoms
Iron (Fe) 2 atoms

Manganese Binding Sites:

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

Manganese binding site 1 out of 3 in 7me3

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Yfea Oligomer Crystal 3, Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:4.5
occ:0.10
ZN A:ZN403 0.2 3.7 0.5
FE A:FE401 0.3 4.6 0.4
OE1 A:GLU207 1.9 5.8 1.0
NE2 A:HIS141 2.1 6.1 1.0
NE2 A:HIS76 2.2 6.3 1.0
OD2 A:ASP282 2.3 10.3 1.0
OD1 A:ASP282 2.5 6.6 1.0
OE2 A:GLU207 2.5 8.8 1.0
CD A:GLU207 2.5 8.8 1.0
CG A:ASP282 2.8 8.2 1.0
CE1 A:HIS76 3.0 6.3 1.0
CE1 A:HIS141 3.1 6.3 1.0
CD2 A:HIS141 3.1 5.8 1.0
CD2 A:HIS76 3.2 6.9 1.0
O A:HOH546 3.9 14.6 1.0
ND2 A:ASN228 3.9 11.5 1.0
CG A:GLU207 4.0 8.2 1.0
ND1 A:HIS76 4.2 6.6 1.0
ND1 A:HIS141 4.2 6.2 1.0
CB A:ALA209 4.2 7.5 1.0
CG A:HIS141 4.2 5.8 1.0
CB A:ASP282 4.3 7.7 1.0
CG A:HIS76 4.3 7.4 1.0
CG A:ASN228 4.3 9.6 1.0
O A:HOH513 4.4 15.9 1.0
OD1 A:ASN228 4.7 12.4 1.0
CB A:GLU207 4.8 9.2 1.0
CB A:ASN228 4.8 8.2 1.0

Manganese binding site 2 out of 3 in 7me3

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Yfea Oligomer Crystal 3, Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:5.2
occ:0.11
FE B:FE401 0.2 4.9 0.2
ZN B:ZN403 0.5 6.4 0.7
NE2 B:HIS76 1.9 6.8 1.0
NE2 B:HIS141 2.0 6.3 1.0
OD2 B:ASP282 2.3 8.8 1.0
OE1 B:GLU207 2.4 9.1 1.0
OE2 B:GLU207 2.6 13.1 1.0
OD1 B:ASP282 2.6 8.0 1.0
CG B:ASP282 2.8 9.6 1.0
CD B:GLU207 2.8 13.5 1.0
CE1 B:HIS76 2.8 9.2 1.0
CE1 B:HIS141 3.0 7.1 1.0
CD2 B:HIS76 3.0 7.2 1.0
CD2 B:HIS141 3.0 5.9 1.0
ND2 B:ASN228 3.8 16.5 1.0
ND1 B:HIS76 4.0 9.0 1.0
CG B:HIS76 4.1 10.1 1.0
ND1 B:HIS141 4.1 6.3 1.0
CG B:HIS141 4.2 9.5 1.0
CG B:GLU207 4.3 9.5 1.0
CB B:ASP282 4.3 6.2 1.0
CB B:ALA209 4.3 7.1 1.0
CG B:ASN228 4.4 16.9 1.0
O B:HOH514 4.4 10.9 1.0
O B:HOH518 4.6 14.7 1.0
CD1 B:LEU101 4.8 9.5 1.0
CB B:ASN228 4.9 12.7 1.0

Manganese binding site 3 out of 3 in 7me3

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Yfea Oligomer Crystal 3, Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn404

b:27.2
occ:0.16
ZN B:ZN405 0.4 27.1 0.8
ND1 B:HIS163 2.5 22.1 1.0
CG B:HIS163 3.5 18.3 1.0
CE1 B:HIS163 3.5 26.4 1.0
CB B:HIS163 3.6 10.2 1.0
CA B:HIS163 3.9 16.0 1.0
O B:HIS163 4.4 23.2 1.0
CG B:PRO116 4.4 19.5 1.0
NE2 B:HIS163 4.6 19.4 1.0
CD2 B:HIS163 4.6 12.3 1.0
C B:HIS163 4.7 14.1 1.0
O B:GLU162 5.0 20.1 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: Sun Oct 6 10:04:37 2024

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