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Manganese in PDB 4pca: X-Ray Crystal Structure of An O-Methyltransferase From Anaplasma Phagocytophilum Bound to Sah and Manganese

Protein crystallography data

The structure of X-Ray Crystal Structure of An O-Methyltransferase From Anaplasma Phagocytophilum Bound to Sah and Manganese, PDB code: 4pca was solved by J.W.Fairman, J.Abendroth, D.Lorimer, T.E.Edwards, Seattle Structuralgenomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.58 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.210, 102.760, 103.320, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 17.2

Manganese Binding Sites:

The binding sites of Manganese atom in the X-Ray Crystal Structure of An O-Methyltransferase From Anaplasma Phagocytophilum Bound to Sah and Manganese (pdb code 4pca). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the X-Ray Crystal Structure of An O-Methyltransferase From Anaplasma Phagocytophilum Bound to Sah and Manganese, PDB code: 4pca:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4pca

Go back to Manganese Binding Sites List in 4pca
Manganese binding site 1 out of 4 in the X-Ray Crystal Structure of An O-Methyltransferase From Anaplasma Phagocytophilum Bound to Sah and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Crystal Structure of An O-Methyltransferase From Anaplasma Phagocytophilum Bound to Sah and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:9.1
occ:1.00
OD1 A:ASP136 2.1 9.8 1.0
OD2 A:ASP162 2.1 8.0 1.0
O A:HOH412 2.2 10.2 1.0
OD1 A:ASN163 2.2 8.2 1.0
O A:HOH443 2.2 13.6 1.0
O A:HOH501 2.2 16.9 1.0
CG A:ASP136 3.1 11.2 1.0
CG A:ASN163 3.1 8.7 1.0
CG A:ASP162 3.1 8.8 1.0
OD2 A:ASP136 3.4 10.1 1.0
ND2 A:ASN163 3.4 9.6 1.0
CB A:ASP162 3.4 8.7 1.0
O A:ALA38 3.8 12.8 1.0
NZ A:LYS139 4.0 11.3 1.0
OD1 A:ASP162 4.3 9.3 1.0
CB A:ASP136 4.5 7.7 1.0
CB A:ASN163 4.5 8.9 1.0
O A:ASP136 4.5 9.9 1.0
C A:ASP162 4.6 7.7 1.0
CA A:ASP162 4.6 7.8 1.0
N A:ASN163 4.7 7.0 1.0
CD2 A:LEU40 4.8 9.0 1.0
CA A:ASP136 4.8 6.6 1.0
CE A:LYS139 4.9 11.5 1.0
C A:ALA38 4.9 11.0 1.0
OH A:TYR142 5.0 9.8 1.0
O A:ASP162 5.0 8.7 1.0

Manganese binding site 2 out of 4 in 4pca

Go back to Manganese Binding Sites List in 4pca
Manganese binding site 2 out of 4 in the X-Ray Crystal Structure of An O-Methyltransferase From Anaplasma Phagocytophilum Bound to Sah and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Crystal Structure of An O-Methyltransferase From Anaplasma Phagocytophilum Bound to Sah and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:9.2
occ:1.00
OD1 B:ASP136 2.1 8.8 1.0
OD2 B:ASP162 2.1 9.4 1.0
O B:HOH412 2.2 10.5 1.0
O B:HOH486 2.2 10.3 1.0
OD1 B:ASN163 2.2 9.6 1.0
O B:HOH431 2.3 13.3 1.0
CG B:ASP136 3.1 9.2 1.0
CG B:ASP162 3.1 9.0 1.0
CG B:ASN163 3.2 9.1 1.0
OD2 B:ASP136 3.4 9.7 1.0
ND2 B:ASN163 3.4 9.6 1.0
CB B:ASP162 3.5 8.1 1.0
O B:ALA38 3.7 11.4 1.0
NZ B:LYS139 4.0 12.3 1.0
OD1 B:ASP162 4.2 9.2 1.0
NH1 B:ARG2 4.4 12.2 1.0
NH2 B:ARG2 4.4 11.9 1.0
CB B:ASP136 4.4 9.3 1.0
O B:ASP136 4.5 9.4 1.0
CB B:ASN163 4.5 9.2 1.0
C B:ASP162 4.6 8.5 1.0
CA B:ASP162 4.6 7.9 1.0
CD2 B:LEU40 4.7 9.2 1.0
CA B:ASP136 4.8 7.0 1.0
N B:ASN163 4.8 8.6 1.0
CZ B:ARG2 4.9 11.2 1.0
OH B:TYR142 4.9 8.8 1.0
O B:ASP162 4.9 8.8 1.0
C B:ALA38 4.9 11.2 1.0
C B:ASP136 5.0 9.8 1.0
CE B:LYS139 5.0 13.0 1.0

Manganese binding site 3 out of 4 in 4pca

Go back to Manganese Binding Sites List in 4pca
Manganese binding site 3 out of 4 in the X-Ray Crystal Structure of An O-Methyltransferase From Anaplasma Phagocytophilum Bound to Sah and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Crystal Structure of An O-Methyltransferase From Anaplasma Phagocytophilum Bound to Sah and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn301

b:9.3
occ:1.00
OD1 C:ASP136 2.1 10.8 1.0
OD2 C:ASP162 2.2 10.1 1.0
O C:HOH407 2.2 10.0 1.0
OD1 C:ASN163 2.2 10.1 1.0
CG C:ASP136 3.1 11.5 1.0
CG C:ASN163 3.1 9.4 1.0
CG C:ASP162 3.1 9.7 1.0
OD2 C:ASP136 3.4 11.0 1.0
ND2 C:ASN163 3.4 9.3 1.0
CB C:ASP162 3.5 11.4 1.0
O C:ALA38 3.7 12.4 1.0
NZ C:LYS139 4.0 14.1 1.0
OD1 C:ASP162 4.3 10.0 1.0
NH1 C:ARG2 4.3 14.8 1.0
NH2 C:ARG2 4.4 12.7 1.0
O C:ASP136 4.4 12.2 1.0
CB C:ASP136 4.5 9.6 1.0
CB C:ASN163 4.5 7.5 1.0
C C:ASP162 4.6 8.5 1.0
CA C:ASP162 4.6 8.7 1.0
CA C:ASP136 4.8 9.1 1.0
N C:ASN163 4.8 8.2 1.0
CD2 C:LEU40 4.8 10.7 1.0
CZ C:ARG2 4.8 13.1 1.0
OH C:TYR142 4.9 11.4 1.0
O C:ASP162 4.9 9.4 1.0
C C:ALA38 4.9 12.5 1.0
C C:ASP136 4.9 11.2 1.0
CE C:LYS139 5.0 14.0 1.0

Manganese binding site 4 out of 4 in 4pca

Go back to Manganese Binding Sites List in 4pca
Manganese binding site 4 out of 4 in the X-Ray Crystal Structure of An O-Methyltransferase From Anaplasma Phagocytophilum Bound to Sah and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Crystal Structure of An O-Methyltransferase From Anaplasma Phagocytophilum Bound to Sah and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:10.7
occ:1.00
OD1 D:ASP136 2.1 11.6 1.0
OD2 D:ASP162 2.2 10.6 1.0
O D:HOH421 2.2 22.6 1.0
O D:HOH405 2.2 11.1 1.0
OD1 D:ASN163 2.3 10.3 1.0
O D:HOH450 2.3 16.4 1.0
CG D:ASP136 3.1 10.3 1.0
CG D:ASP162 3.1 10.8 1.0
CG D:ASN163 3.2 10.5 1.0
OD2 D:ASP136 3.3 12.5 1.0
ND2 D:ASN163 3.4 11.8 1.0
CB D:ASP162 3.5 9.8 1.0
O D:ALA38 3.8 14.0 1.0
NZ D:LYS139 4.0 15.3 1.0
OD1 D:ASP162 4.2 10.7 1.0
CB D:ASP136 4.4 8.9 1.0
CB D:ASN163 4.6 9.6 1.0
O D:ASP136 4.6 12.3 1.0
C D:ASP162 4.7 11.1 1.0
CD2 D:LEU40 4.7 11.1 1.0
CA D:ASP162 4.7 8.9 1.0
CA D:ASP136 4.8 9.6 1.0
CE D:LYS139 4.8 20.0 1.0
N D:ASN163 4.8 8.3 1.0
C D:ALA38 5.0 12.5 1.0

Reference:

J.W.Fairman, J.Abendroth, D.Lorimer, T.E.Edwards. X-Ray Crystal Structure of An O-Methyltransferase From Anaplasma Phagocytophilum Bound to Sah and Manganese To Be Published.
Page generated: Tue Dec 15 04:26:00 2020

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