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Manganese in PDB 3nio: Crystal Structure of Pseudomonas Aeruginosa Guanidinobutyrase

Enzymatic activity of Crystal Structure of Pseudomonas Aeruginosa Guanidinobutyrase

All present enzymatic activity of Crystal Structure of Pseudomonas Aeruginosa Guanidinobutyrase:
3.5.3.7;

Protein crystallography data

The structure of Crystal Structure of Pseudomonas Aeruginosa Guanidinobutyrase, PDB code: 3nio was solved by S.J.Lee, H.S.Kim, D.J.Kim, H.J.Yoon, K.H.Kim, J.Y.Yoon, J.Y.Jang, H.Im, D.An, S.W.Suh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.047, 158.954, 84.547, 90.00, 114.84, 90.00
R / Rfree (%) 23.3 / 25.1

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Pseudomonas Aeruginosa Guanidinobutyrase (pdb code 3nio). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the Crystal Structure of Pseudomonas Aeruginosa Guanidinobutyrase, PDB code: 3nio:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in 3nio

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Manganese binding site 1 out of 12 in the Crystal Structure of Pseudomonas Aeruginosa Guanidinobutyrase


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 Pseudomonas Aeruginosa Guanidinobutyrase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1601

b:19.5
occ:1.00
 O A:HOH1061 2.3 23.0 1.0
O A:HOH624 2.4 17.4 1.0
OD2 A:ASP152 2.4 16.9 1.0
ND1 A:HIS129 2.4 18.0 1.0
OD2 A:ASP243 2.5 17.8 1.0
OD2 A:ASP156 2.5 21.9 1.0
CE1 A:HIS129 3.1 18.5 1.0
CG A:ASP152 3.4 17.9 1.0
MN A:MN1602 3.4 16.4 1.0
CG A:ASP243 3.5 18.3 1.0
CG A:ASP156 3.6 21.9 1.0
CG A:HIS129 3.6 18.1 1.0
OD1 A:ASP152 3.7 17.0 1.0
OD1 A:ASP156 3.9 21.3 1.0
CB A:ASP243 3.9 17.6 1.0
CB A:HIS129 4.1 18.1 1.0
NE2 A:HIS129 4.3 18.5 1.0
CD2 A:HIS129 4.6 18.2 1.0
OD1 A:ASP243 4.6 17.9 1.0
CB A:ASP152 4.8 18.3 1.0
CB A:ASP156 4.9 21.8 1.0
O A:HIS168 4.9 23.9 1.0
OE2 A:GLU287 5.0 18.2 1.0

Manganese binding site 2 out of 12 in 3nio

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Manganese binding site 2 out of 12 in the Crystal Structure of Pseudomonas Aeruginosa Guanidinobutyrase


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 Pseudomonas Aeruginosa Guanidinobutyrase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1602

b:16.4
occ:1.00
 O A:HOH624 2.2 17.4 1.0
ND1 A:HIS154 2.2 19.1 1.0
OD1 A:ASP152 2.3 17.0 1.0
OD2 A:ASP245 2.4 17.5 1.0
OD1 A:ASP245 2.6 17.4 1.0
OD2 A:ASP243 2.7 17.8 1.0
CG A:ASP245 2.9 17.7 1.0
CE1 A:HIS154 3.0 19.3 1.0
CG A:ASP152 3.2 17.9 1.0
CG A:HIS154 3.3 19.6 1.0
MN A:MN1601 3.4 19.5 1.0
OD2 A:ASP152 3.5 16.9 1.0
CG A:ASP243 3.7 18.3 1.0
CB A:HIS154 3.8 19.7 1.0
N A:HIS154 3.9 19.4 1.0
N A:ALA153 4.1 18.9 1.0
O A:HOH1061 4.2 23.0 1.0
NE2 A:HIS154 4.2 19.3 1.0
OD1 A:ASP243 4.3 17.9 1.0
CB A:ASP245 4.4 17.6 1.0
CD2 A:HIS154 4.4 19.3 1.0
CA A:HIS154 4.5 19.8 1.0
C A:ALA153 4.6 19.2 1.0
CB A:ASP152 4.6 18.3 1.0
CB A:ASP243 4.6 17.6 1.0
CB A:ALA153 4.6 19.0 1.0
OG1 A:THR257 4.7 17.8 1.0
CA A:ALA153 4.7 19.0 1.0
OD1 A:ASP156 4.9 21.3 1.0
OD2 A:ASP156 5.0 21.9 1.0
CA A:ASP152 5.0 18.5 1.0

Manganese binding site 3 out of 12 in 3nio

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Manganese binding site 3 out of 12 in the Crystal Structure of Pseudomonas Aeruginosa Guanidinobutyrase


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 Pseudomonas Aeruginosa Guanidinobutyrase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1603

b:15.8
occ:1.00
 O B:HOH1060 2.2 29.5 1.0
OD2 B:ASP152 2.3 16.9 1.0
O B:HOH791 2.4 14.5 1.0
OD2 B:ASP243 2.4 17.3 1.0
ND1 B:HIS129 2.4 18.4 1.0
OD2 B:ASP156 2.5 19.5 1.0
CE1 B:HIS129 3.1 18.5 1.0
CG B:ASP152 3.4 17.5 1.0
MN B:MN1604 3.5 14.4 1.0
CG B:ASP243 3.5 17.3 1.0
CG B:HIS129 3.5 17.9 1.0
CG B:ASP156 3.6 19.5 1.0
OD1 B:ASP152 3.7 17.2 1.0
OD1 B:ASP156 3.9 18.9 1.0
CB B:ASP243 4.0 16.9 1.0
CB B:HIS129 4.0 17.7 1.0
NE2 B:HIS129 4.3 19.1 1.0
CD2 B:HIS129 4.5 18.5 1.0
OD1 B:ASP243 4.6 17.0 1.0
CB B:ASP152 4.7 17.7 1.0
CB B:ASP156 4.9 19.6 1.0
OE2 B:GLU287 4.9 17.8 1.0
O B:HIS168 5.0 22.6 1.0
NE2 B:HIS150 5.0 18.4 1.0

Manganese binding site 4 out of 12 in 3nio

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Manganese binding site 4 out of 12 in the Crystal Structure of Pseudomonas Aeruginosa Guanidinobutyrase


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 Pseudomonas Aeruginosa Guanidinobutyrase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1604

b:14.4
occ:1.00
 O B:HOH791 2.2 14.5 1.0
OD1 B:ASP152 2.2 17.2 1.0
ND1 B:HIS154 2.3 18.0 1.0
OD2 B:ASP245 2.3 16.1 1.0
OD1 B:ASP245 2.6 15.9 1.0
CG B:ASP245 2.8 16.4 1.0
OD2 B:ASP243 2.8 17.3 1.0
CE1 B:HIS154 3.1 18.5 1.0
CG B:ASP152 3.2 17.5 1.0
CG B:HIS154 3.4 18.2 1.0
MN B:MN1603 3.5 15.8 1.0
OD2 B:ASP152 3.5 16.9 1.0
CG B:ASP243 3.7 17.3 1.0
CB B:HIS154 3.9 18.1 1.0
N B:HIS154 4.0 17.9 1.0
O B:HOH1060 4.1 29.5 1.0
N B:ALA153 4.1 17.7 1.0
OD1 B:ASP243 4.2 17.0 1.0
NE2 B:HIS154 4.3 18.7 1.0
CB B:ASP245 4.3 16.5 1.0
CD2 B:HIS154 4.5 18.4 1.0
CA B:HIS154 4.6 18.1 1.0
CB B:ASP152 4.6 17.7 1.0
OG1 B:THR257 4.6 17.4 1.0
CB B:ASP243 4.6 16.9 1.0
CB B:ALA153 4.7 17.8 1.0
C B:ALA153 4.7 17.9 1.0
CA B:ALA153 4.7 17.8 1.0
OD1 B:ASP156 4.9 18.9 1.0
OD2 B:ASP156 5.0 19.5 1.0
CA B:ASP152 5.0 17.6 1.0

Manganese binding site 5 out of 12 in 3nio

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Manganese binding site 5 out of 12 in the Crystal Structure of Pseudomonas Aeruginosa Guanidinobutyrase


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 Pseudomonas Aeruginosa Guanidinobutyrase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1605

b:19.0
occ:1.00
 O C:HOH1007 2.3 14.2 1.0
ND1 C:HIS129 2.4 18.7 1.0
OD2 C:ASP152 2.4 20.8 1.0
OD2 C:ASP243 2.4 18.2 1.0
O C:HOH1059 2.4 24.2 1.0
OD2 C:ASP156 2.5 22.9 1.0
CE1 C:HIS129 3.1 19.0 1.0
MN C:MN1606 3.4 17.5 1.0
CG C:ASP152 3.4 20.8 1.0
CG C:ASP156 3.5 23.2 1.0
CG C:ASP243 3.5 18.9 1.0
CG C:HIS129 3.5 19.3 1.0
OD1 C:ASP152 3.7 20.5 1.0
OD1 C:ASP156 3.8 22.6 1.0
CB C:ASP243 4.0 18.8 1.0
CB C:HIS129 4.0 19.5 1.0
NE2 C:HIS129 4.3 19.1 1.0
CD2 C:HIS129 4.5 19.4 1.0
OD1 C:ASP243 4.6 18.1 1.0
CB C:ASP152 4.8 20.7 1.0
CB C:ASP156 4.9 23.3 1.0
O C:HIS168 4.9 26.8 1.0

Manganese binding site 6 out of 12 in 3nio

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Manganese binding site 6 out of 12 in the Crystal Structure of Pseudomonas Aeruginosa Guanidinobutyrase


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 Pseudomonas Aeruginosa Guanidinobutyrase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1606

b:17.5
occ:1.00
 O C:HOH1007 2.2 14.2 1.0
OD1 C:ASP152 2.3 20.5 1.0
ND1 C:HIS154 2.3 21.1 1.0
OD2 C:ASP245 2.3 18.0 1.0
OD2 C:ASP243 2.6 18.2 1.0
OD1 C:ASP245 2.6 18.1 1.0
CG C:ASP245 2.8 18.4 1.0
CE1 C:HIS154 3.1 21.5 1.0
CG C:ASP152 3.2 20.8 1.0
CG C:HIS154 3.4 21.6 1.0
MN C:MN1605 3.4 19.0 1.0
OD2 C:ASP152 3.5 20.8 1.0
CG C:ASP243 3.5 18.9 1.0
CB C:HIS154 3.8 21.6 1.0
OD1 C:ASP243 4.0 18.1 1.0
N C:HIS154 4.1 21.4 1.0
O C:HOH1059 4.2 24.2 1.0
N C:ALA153 4.2 20.9 1.0
NE2 C:HIS154 4.3 21.5 1.0
CB C:ASP245 4.3 18.5 1.0
CD2 C:HIS154 4.4 21.5 1.0
CB C:ASP243 4.5 18.8 1.0
CA C:HIS154 4.5 21.7 1.0
CB C:ASP152 4.6 20.7 1.0
OG1 C:THR257 4.6 19.6 1.0
C C:ALA153 4.8 21.3 1.0
CB C:ALA153 4.8 21.1 1.0
CA C:ALA153 4.8 21.1 1.0
OD1 C:ASP156 4.9 22.6 1.0

Manganese binding site 7 out of 12 in 3nio

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Manganese binding site 7 out of 12 in the Crystal Structure of Pseudomonas Aeruginosa Guanidinobutyrase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Pseudomonas Aeruginosa Guanidinobutyrase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1607

b:16.1
occ:1.00
 O D:HOH1058 2.3 29.0 1.0
OD2 D:ASP152 2.4 19.9 1.0
O D:HOH1040 2.4 11.8 1.0
OD2 D:ASP243 2.4 16.8 1.0
OD2 D:ASP156 2.5 21.6 1.0
ND1 D:HIS129 2.5 19.0 1.0
CE1 D:HIS129 3.2 19.2 1.0
CG D:ASP152 3.4 20.6 1.0
MN D:MN1608 3.4 16.0 1.0
CG D:ASP243 3.5 17.6 1.0
CG D:ASP156 3.5 21.8 1.0
CG D:HIS129 3.6 18.8 1.0
OD1 D:ASP152 3.7 21.1 1.0
OD1 D:ASP156 3.9 20.7 1.0
CB D:ASP243 4.0 17.5 1.0
CB D:HIS129 4.0 18.6 1.0
NE2 D:HIS129 4.4 19.2 1.0
OD1 D:ASP243 4.5 17.6 1.0
CD2 D:HIS129 4.6 18.9 1.0
CB D:ASP152 4.8 20.4 1.0
CB D:ASP156 4.8 21.9 1.0
O D:HIS168 4.9 24.1 1.0

Manganese binding site 8 out of 12 in 3nio

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Manganese binding site 8 out of 12 in the Crystal Structure of Pseudomonas Aeruginosa Guanidinobutyrase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Pseudomonas Aeruginosa Guanidinobutyrase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1608

b:16.0
occ:1.00
 O D:HOH1040 2.2 11.8 1.0
OD1 D:ASP152 2.3 21.1 1.0
OD2 D:ASP245 2.4 16.5 1.0
ND1 D:HIS154 2.4 20.0 1.0
OD2 D:ASP243 2.5 16.8 1.0
OD1 D:ASP245 2.6 15.9 1.0
CG D:ASP245 2.9 16.6 1.0
CE1 D:HIS154 3.2 20.4 1.0
CG D:ASP152 3.3 20.6 1.0
MN D:MN1607 3.4 16.1 1.0
CG D:ASP243 3.5 17.6 1.0
CG D:HIS154 3.5 20.5 1.0
OD2 D:ASP152 3.5 19.9 1.0
CB D:HIS154 3.9 20.6 1.0
OD1 D:ASP243 4.0 17.6 1.0
N D:HIS154 4.0 20.5 1.0
N D:ALA153 4.1 20.4 1.0
O D:HOH1058 4.2 29.0 1.0
CB D:ASP245 4.4 16.5 1.0
NE2 D:HIS154 4.4 20.4 1.0
CB D:ASP243 4.5 17.5 1.0
CD2 D:HIS154 4.6 20.4 1.0
CA D:HIS154 4.6 20.6 1.0
CB D:ALA153 4.6 20.4 1.0
CB D:ASP152 4.6 20.4 1.0
CA D:ALA153 4.7 20.4 1.0
C D:ALA153 4.7 20.4 1.0
OG1 D:THR257 4.7 17.8 1.0
OD1 D:ASP156 4.9 20.7 1.0
CA D:ASP152 4.9 20.4 1.0
OD2 D:ASP156 5.0 21.6 1.0
C D:ASP152 5.0 20.4 1.0

Manganese binding site 9 out of 12 in 3nio

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Manganese binding site 9 out of 12 in the Crystal Structure of Pseudomonas Aeruginosa Guanidinobutyrase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of Pseudomonas Aeruginosa Guanidinobutyrase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn1609

b:20.1
occ:1.00
 O E:HOH1057 2.2 29.5 1.0
ND1 E:HIS129 2.4 20.8 1.0
OD2 E:ASP156 2.4 22.7 1.0
OD2 E:ASP152 2.5 20.7 1.0
O E:HOH1033 2.5 15.2 1.0
OD2 E:ASP243 2.5 22.0 1.0
CE1 E:HIS129 3.1 21.1 1.0
MN E:MN1610 3.4 18.8 1.0
CG E:ASP152 3.4 20.8 1.0
CG E:ASP156 3.5 23.0 1.0
CG E:ASP243 3.5 21.6 1.0
CG E:HIS129 3.5 21.0 1.0
OD1 E:ASP152 3.7 20.1 1.0
OD1 E:ASP156 3.9 22.6 1.0
CB E:HIS129 4.0 20.9 1.0
CB E:ASP243 4.0 21.3 1.0
NE2 E:HIS129 4.3 20.9 1.0
OD1 E:ASP243 4.5 21.8 1.0
CD2 E:HIS129 4.5 21.1 1.0
CB E:ASP152 4.8 20.5 1.0
CB E:ASP156 4.8 23.0 1.0
O E:HIS168 4.9 25.7 1.0
OD2 E:ASP245 5.0 20.4 1.0

Manganese binding site 10 out of 12 in 3nio

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Manganese binding site 10 out of 12 in the Crystal Structure of Pseudomonas Aeruginosa Guanidinobutyrase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of Pseudomonas Aeruginosa Guanidinobutyrase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn1610

b:18.8
occ:1.00
 O E:HOH1033 2.1 15.2 1.0
OD1 E:ASP152 2.3 20.1 1.0
ND1 E:HIS154 2.3 20.7 1.0
OD2 E:ASP245 2.5 20.4 1.0
OD2 E:ASP243 2.6 22.0 1.0
OD1 E:ASP245 2.6 19.7 1.0
CG E:ASP245 2.9 20.0 1.0
CE1 E:HIS154 3.1 20.7 1.0
CG E:ASP152 3.2 20.8 1.0
MN E:MN1609 3.4 20.1 1.0
CG E:HIS154 3.4 20.9 1.0
OD2 E:ASP152 3.5 20.7 1.0
CG E:ASP243 3.6 21.6 1.0
CB E:HIS154 3.8 21.0 1.0
N E:HIS154 4.0 20.9 1.0
O E:HOH1057 4.1 29.5 1.0
N E:ALA153 4.2 20.7 1.0
OD1 E:ASP243 4.2 21.8 1.0
NE2 E:HIS154 4.3 20.9 1.0
CB E:ASP245 4.4 20.0 1.0
CD2 E:HIS154 4.4 20.9 1.0
CA E:HIS154 4.5 21.1 1.0
CB E:ASP243 4.6 21.3 1.0
CB E:ASP152 4.6 20.5 1.0
OG1 E:THR257 4.7 20.4 1.0
C E:ALA153 4.7 20.9 1.0
CB E:ALA153 4.7 20.9 1.0
CA E:ALA153 4.7 20.8 1.0
OD2 E:ASP156 4.8 22.7 1.0
OD1 E:ASP156 4.9 22.6 1.0
CA E:ASP152 5.0 20.6 1.0

Reference:

S.J.Lee, D.J.Kim, H.S.Kim, B.I.Lee, H.J.Yoon, J.Y.Yoon, K.H.Kim, J.Y.Jang, H.N.Im, D.R.An, J.S.Song, H.J.Kim, S.W.Suh. Crystal Structures of Pseudomonas Aeruginosa Guanidinobutyrase and Guanidinopropionase, Members of the Ureohydrolase Superfamily J.Struct.Biol. V. 175 329 2011.
ISSN: ISSN 1047-8477
PubMed: 21600989
DOI: 10.1016/J.JSB.2011.05.002
Page generated: Sat Oct 5 17:19:53 2024

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