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Manganese in PDB 3nqb: Crystal Structure of Adenine Deaminase From Agrobacterium Tumefaciens (Str. C 58)

Enzymatic activity of Crystal Structure of Adenine Deaminase From Agrobacterium Tumefaciens (Str. C 58)

All present enzymatic activity of Crystal Structure of Adenine Deaminase From Agrobacterium Tumefaciens (Str. C 58):
3.5.4.2;

Protein crystallography data

The structure of Crystal Structure of Adenine Deaminase From Agrobacterium Tumefaciens (Str. C 58), PDB code: 3nqb was solved by A.Bagaria, D.Kumaran, S.K.Burley, S.Swaminathan, New York Sgx Researchcenter For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.74 / 2.21
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.101, 130.970, 69.999, 90.00, 97.98, 90.00
R / Rfree (%) 17.2 / 23.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Adenine Deaminase From Agrobacterium Tumefaciens (Str. C 58) (pdb code 3nqb). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of Adenine Deaminase From Agrobacterium Tumefaciens (Str. C 58), PDB code: 3nqb:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 3nqb

Go back to Manganese Binding Sites List in 3nqb
Manganese binding site 1 out of 6 in the Crystal Structure of Adenine Deaminase From Agrobacterium Tumefaciens (Str. C 58)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Adenine Deaminase From Agrobacterium Tumefaciens (Str. C 58) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn606

b:24.2
occ:1.00
 OE1 A:GLU187 2.1 20.8 1.0
O A:HOH751 2.2 19.8 1.0
OE2 A:GLU240 2.2 19.9 1.0
NE2 A:HIS239 2.2 15.7 1.0
ND1 A:HIS218 2.4 21.1 1.0
O A:HOH760 2.4 25.4 1.0
CE1 A:HIS218 3.2 17.2 1.0
CE1 A:HIS239 3.2 16.4 1.0
CD A:GLU240 3.2 16.8 1.0
CD2 A:HIS239 3.2 22.1 1.0
CD A:GLU187 3.3 19.9 1.0
CG A:HIS218 3.5 21.4 1.0
CG A:GLU240 3.5 16.8 1.0
OE2 A:GLU187 3.7 21.1 1.0
CB A:HIS218 3.8 19.6 1.0
MN A:MN607 4.0 20.9 1.0
ND1 A:HIS239 4.3 17.4 1.0
OE1 A:GLU240 4.4 16.0 1.0
CG A:HIS239 4.4 17.4 1.0
NE2 A:HIS218 4.4 20.0 1.0
O A:HOH617 4.4 29.3 1.0
CG A:GLU187 4.5 19.5 1.0
CD2 A:HIS218 4.5 22.9 1.0
CA A:HIS218 4.6 21.0 1.0
NH1 A:ARG260 4.6 19.4 1.0
OD2 A:ASP289 4.7 15.3 1.0
CB A:GLU187 4.8 21.0 1.0
NE2 A:HIS92 4.9 21.7 1.0

Manganese binding site 2 out of 6 in 3nqb

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Manganese binding site 2 out of 6 in the Crystal Structure of Adenine Deaminase From Agrobacterium Tumefaciens (Str. C 58)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Adenine Deaminase From Agrobacterium Tumefaciens (Str. C 58) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn607

b:20.9
occ:1.00
 NE2 A:HIS94 2.1 17.5 1.0
OD1 A:ASP289 2.2 18.9 1.0
O A:HOH617 2.2 29.3 1.0
NE2 A:HIS92 2.3 21.7 1.0
O A:HOH751 2.4 19.8 1.0
OE2 A:GLU187 2.4 21.1 1.0
CE1 A:HIS94 3.1 16.9 1.0
CE1 A:HIS92 3.1 21.7 1.0
CD2 A:HIS94 3.2 16.7 1.0
CG A:ASP289 3.2 17.8 1.0
CD A:GLU187 3.3 19.9 1.0
CD2 A:HIS92 3.4 17.4 1.0
OE1 A:GLU187 3.6 20.8 1.0
OD2 A:ASP289 3.6 15.3 1.0
NE2 A:HIS239 4.0 15.7 1.0
MN A:MN606 4.0 24.2 1.0
CE1 A:HIS239 4.2 16.4 1.0
O A:HOH760 4.2 25.4 1.0
ND1 A:HIS94 4.2 18.7 1.0
ND1 A:HIS92 4.3 20.8 1.0
CG A:HIS94 4.3 17.7 1.0
CG A:HIS92 4.5 19.3 1.0
CG A:GLU187 4.5 19.5 1.0
CB A:ASP289 4.6 16.4 1.0
CD2 A:HIS239 4.6 22.1 1.0
CA A:ASP289 4.8 17.6 1.0
CE1 A:HIS122 4.8 20.6 1.0
ND1 A:HIS239 5.0 17.4 1.0

Manganese binding site 3 out of 6 in 3nqb

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Manganese binding site 3 out of 6 in the Crystal Structure of Adenine Deaminase From Agrobacterium Tumefaciens (Str. C 58)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Adenine Deaminase From Agrobacterium Tumefaciens (Str. C 58) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn608

b:26.8
occ:1.00
 OD1 A:ASP478 2.2 16.7 1.0
ND1 A:HIS477 2.2 20.5 1.0
OE2 A:GLU123 2.3 26.2 1.0
OE1 A:GLU123 2.3 23.0 1.0
NE2 A:HIS122 2.3 17.8 1.0
CD A:GLU123 2.6 24.8 1.0
CE1 A:HIS477 3.1 19.9 1.0
CD2 A:HIS122 3.2 17.7 1.0
CG A:ASP478 3.2 18.9 1.0
CG A:HIS477 3.3 20.3 1.0
CE1 A:HIS122 3.3 20.6 1.0
OD2 A:ASP478 3.7 18.7 1.0
CB A:HIS477 3.7 18.4 1.0
CG A:GLU123 4.1 18.4 1.0
NE2 A:HIS477 4.2 19.9 1.0
CG A:HIS122 4.3 18.6 1.0
CB A:ASP478 4.4 17.3 1.0
CD2 A:HIS477 4.4 23.1 1.0
ND1 A:HIS122 4.4 22.0 1.0
CA A:HIS477 4.4 19.5 1.0
NE2 A:HIS480 4.4 22.6 1.0
CA A:ASP478 4.5 17.6 1.0
CE1 A:HIS480 4.7 19.8 1.0

Manganese binding site 4 out of 6 in 3nqb

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Manganese binding site 4 out of 6 in the Crystal Structure of Adenine Deaminase From Agrobacterium Tumefaciens (Str. C 58)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Adenine Deaminase From Agrobacterium Tumefaciens (Str. C 58) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn606

b:23.5
occ:1.00
 NE2 B:HIS94 2.1 18.9 1.0
OD1 B:ASP289 2.2 17.2 1.0
NE2 B:HIS92 2.2 18.8 1.0
OE2 B:GLU187 2.2 22.5 1.0
O B:HOH825 2.4 28.4 1.0
O B:HOH812 2.5 16.3 1.0
CE1 B:HIS92 3.1 20.4 1.0
CE1 B:HIS94 3.1 20.7 1.0
CD2 B:HIS94 3.1 17.9 1.0
CG B:ASP289 3.2 21.3 1.0
CD B:GLU187 3.2 22.4 1.0
CD2 B:HIS92 3.3 19.0 1.0
OD2 B:ASP289 3.4 20.1 1.0
OE1 B:GLU187 3.7 26.9 1.0
NE2 B:HIS239 3.9 22.3 1.0
MN B:MN607 4.0 27.3 1.0
CE1 B:HIS239 4.2 19.3 1.0
ND1 B:HIS94 4.2 16.6 1.0
ND1 B:HIS92 4.2 20.0 1.0
CG B:HIS94 4.3 20.3 1.0
O B:HOH811 4.3 20.4 1.0
CG B:GLU187 4.3 21.4 1.0
CG B:HIS92 4.4 17.6 1.0
CB B:ASP289 4.5 20.3 1.0
CD2 B:HIS239 4.6 22.4 1.0
CA B:ASP289 4.8 20.5 1.0
CE1 B:HIS122 4.9 23.4 1.0
ND1 B:HIS239 4.9 22.1 1.0

Manganese binding site 5 out of 6 in 3nqb

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Manganese binding site 5 out of 6 in the Crystal Structure of Adenine Deaminase From Agrobacterium Tumefaciens (Str. C 58)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Adenine Deaminase From Agrobacterium Tumefaciens (Str. C 58) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn607

b:27.3
occ:1.00
 OE1 B:GLU187 2.1 26.9 1.0
OE2 B:GLU240 2.2 25.6 1.0
NE2 B:HIS239 2.2 22.3 1.0
O B:HOH812 2.3 16.3 1.0
ND1 B:HIS218 2.4 25.9 1.0
O B:HOH811 2.6 20.4 1.0
CD2 B:HIS239 3.1 22.4 1.0
CD B:GLU187 3.1 22.4 1.0
CE1 B:HIS218 3.2 23.8 1.0
CD B:GLU240 3.2 25.3 1.0
CE1 B:HIS239 3.3 19.3 1.0
OE2 B:GLU187 3.4 22.5 1.0
CG B:HIS218 3.5 23.8 1.0
CG B:GLU240 3.5 23.9 1.0
CB B:HIS218 3.9 19.7 1.0
MN B:MN606 4.0 23.5 1.0
CG B:HIS239 4.3 20.9 1.0
OE1 B:GLU240 4.3 26.7 1.0
ND1 B:HIS239 4.4 22.1 1.0
NE2 B:HIS218 4.4 25.8 1.0
CG B:GLU187 4.5 21.4 1.0
CD2 B:HIS218 4.5 25.4 1.0
OD2 B:ASP289 4.6 20.1 1.0
CA B:HIS218 4.6 20.6 1.0
NE2 B:HIS92 4.7 18.8 1.0
O B:HOH825 4.7 28.4 1.0
NH1 B:ARG260 4.8 19.2 1.0
CB B:GLU187 4.8 21.7 1.0

Manganese binding site 6 out of 6 in 3nqb

Go back to Manganese Binding Sites List in 3nqb
Manganese binding site 6 out of 6 in the Crystal Structure of Adenine Deaminase From Agrobacterium Tumefaciens (Str. C 58)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Adenine Deaminase From Agrobacterium Tumefaciens (Str. C 58) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn608

b:29.7
occ:1.00
 OD1 B:ASP478 2.1 26.3 1.0
ND1 B:HIS477 2.2 22.9 1.0
NE2 B:HIS122 2.3 25.3 1.0
OE2 B:GLU123 2.3 19.9 1.0
OE1 B:GLU123 2.4 21.7 1.0
CD B:GLU123 2.7 20.5 1.0
CE1 B:HIS477 3.1 20.4 1.0
CG B:ASP478 3.1 22.9 1.0
CD2 B:HIS122 3.2 20.1 1.0
CE1 B:HIS122 3.2 23.4 1.0
CG B:HIS477 3.3 22.4 1.0
O B:HOH767 3.5 22.0 1.0
OD2 B:ASP478 3.7 24.7 1.0
CB B:HIS477 3.7 20.9 1.0
CG B:GLU123 4.2 21.0 1.0
CB B:ASP478 4.3 21.1 1.0
NE2 B:HIS477 4.3 21.8 1.0
CG B:HIS122 4.3 20.0 1.0
ND1 B:HIS122 4.3 24.6 1.0
CA B:ASP478 4.4 20.5 1.0
CD2 B:HIS477 4.4 20.7 1.0
CE1 B:HIS480 4.4 21.5 1.0
CA B:HIS477 4.4 21.1 1.0
NE2 B:HIS480 4.6 20.4 1.0

Reference:

A.Bagaria, D.Kumaran, S.K.Burley, S.Swaminathan. Crystal Structure of Adenine Deaminase From Agrobacterium Tumefaciens (Str. C 58) To Be Published.
Page generated: Sat Oct 5 17:20:07 2024

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