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Manganese in PDB 2bn7: Mn Substituted E. Coli Aminopeptidase P in Complex with Product and Zn

Enzymatic activity of Mn Substituted E. Coli Aminopeptidase P in Complex with Product and Zn

All present enzymatic activity of Mn Substituted E. Coli Aminopeptidase P in Complex with Product and Zn:
3.4.11.9;

Protein crystallography data

The structure of Mn Substituted E. Coli Aminopeptidase P in Complex with Product and Zn, PDB code: 2bn7 was solved by S.C.Graham, C.S.Bond, H.C.Freeman, J.M.Guss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 119.52 / 2.40
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 139.695, 139.695, 230.674, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 18.7

Other elements in 2bn7:

The structure of Mn Substituted E. Coli Aminopeptidase P in Complex with Product and Zn also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Mn Substituted E. Coli Aminopeptidase P in Complex with Product and Zn (pdb code 2bn7). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Mn Substituted E. Coli Aminopeptidase P in Complex with Product and Zn, PDB code: 2bn7:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 2bn7

Go back to Manganese Binding Sites List in 2bn7
Manganese binding site 1 out of 2 in the Mn Substituted E. Coli Aminopeptidase P in Complex with Product and Zn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Mn Substituted E. Coli Aminopeptidase P in Complex with Product and Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1441

b:41.9
occ:1.00
O A:HOH2284 2.0 42.8 1.0
OE2 A:GLU406 2.1 53.4 1.0
NE2 A:HIS354 2.2 52.6 1.0
OD2 A:ASP271 2.2 52.6 1.0
OE2 A:GLU383 2.4 58.8 1.0
CD A:GLU406 3.1 52.8 1.0
CE1 A:HIS354 3.1 51.0 1.0
CD A:GLU383 3.1 54.4 1.0
CD2 A:HIS354 3.1 52.1 1.0
MN A:MN1442 3.1 47.3 1.0
CG A:ASP271 3.1 53.7 1.0
OE1 A:GLU383 3.3 54.2 1.0
OE1 A:GLU406 3.4 52.1 1.0
OD1 A:ASP271 3.5 58.5 1.0
CG2 A:THR381 3.6 50.7 1.0
OG1 A:THR381 3.8 49.3 1.0
CB A:THR381 3.9 51.9 1.0
ND1 A:HIS354 4.2 49.4 1.0
CG A:HIS354 4.2 49.4 1.0
O A:HOH2286 4.3 58.6 1.0
N A:PRO501 4.3 53.8 1.0
CG A:GLU406 4.4 52.6 1.0
CB A:ASP271 4.4 53.1 1.0
CG A:GLU383 4.4 53.9 1.0
CA A:PRO501 4.5 54.1 1.0
NE2 A:HIS361 4.7 56.5 1.0
O A:HOH2228 4.8 41.4 1.0
CD2 A:HIS361 4.9 56.6 1.0
ZN A:ZN1445 4.9 70.4 0.8

Manganese binding site 2 out of 2 in 2bn7

Go back to Manganese Binding Sites List in 2bn7
Manganese binding site 2 out of 2 in the Mn Substituted E. Coli Aminopeptidase P in Complex with Product and Zn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Mn Substituted E. Coli Aminopeptidase P in Complex with Product and Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1442

b:47.3
occ:1.00
OD1 A:ASP271 2.1 58.5 1.0
OE1 A:GLU406 2.1 52.1 1.0
OD1 A:ASP260 2.2 53.7 1.0
O A:HOH2284 2.2 42.8 1.0
OD2 A:ASP260 2.4 55.6 1.0
CG A:ASP260 2.6 53.5 1.0
CD A:GLU406 3.0 52.8 1.0
CG A:ASP271 3.0 53.7 1.0
MN A:MN1441 3.1 41.9 1.0
OE2 A:GLU406 3.2 53.4 1.0
OD2 A:ASP271 3.2 52.6 1.0
O A:HOH2286 3.3 58.6 1.0
OG1 A:THR273 3.6 50.2 1.0
OH A:TYR229 3.7 48.6 1.0
OE1 A:GLU383 4.1 54.2 1.0
CB A:ASP260 4.1 52.2 1.0
CZ A:TYR229 4.2 49.0 1.0
CG A:GLU406 4.3 52.6 1.0
CB A:ASP271 4.4 53.1 1.0
N A:PRO501 4.5 53.8 1.0
CE2 A:TYR229 4.5 48.5 1.0
C A:ASP271 4.6 52.8 1.0
O A:ILE272 4.6 50.8 1.0
CD A:GLU383 4.7 54.4 1.0
O A:ASP271 4.8 52.6 1.0
C A:ILE272 4.8 50.9 1.0
N A:ILE272 4.8 51.9 1.0
CA A:ASP271 4.8 52.6 1.0
OE2 A:GLU383 4.8 58.8 1.0
CD A:PRO501 4.8 53.3 1.0
NE A:ARG404 4.8 51.9 1.0
CA A:ASP260 4.9 52.6 1.0
CB A:GLU406 4.9 53.1 1.0
CE1 A:TYR229 5.0 49.1 1.0
CB A:THR273 5.0 49.6 1.0

Reference:

S.C.Graham, C.S.Bond, H.C.Freeman, J.M.Guss. Structural and Functional Implications of Metal Ion Selection in Aminopeptidase P, A Metalloprotease with A Dinuclear Metal Center. Biochemistry V. 44 13820 2005.
ISSN: ISSN 0006-2960
PubMed: 16229471
DOI: 10.1021/BI0512849
Page generated: Tue Dec 15 04:00:09 2020

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