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Manganese in PDB 2qjt: Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis

Enzymatic activity of Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis

All present enzymatic activity of Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis:
2.7.7.1;

Protein crystallography data

The structure of Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis, PDB code: 2qjt was solved by N.Huang, L.Sorci, X.Zhang, C.Brautigan, N.Raffaelli, G.Magni, N.V.Grishin, A.Osterman, H.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.61 / 2.30
Space group F 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 125.644, 163.645, 179.967, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 24.9

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis (pdb code 2qjt). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 9 binding sites of Manganese where determined in the Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis, PDB code: 2qjt:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Manganese binding site 1 out of 9 in 2qjt

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Manganese binding site 1 out of 9 in the Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis


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 A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn505

b:34.7
occ:1.00
 O B:HOH676 2.1 29.2 1.0
O B:HOH677 2.2 33.0 1.0
O B:HOH687 2.2 45.6 1.0
OE2 B:GLU250 2.2 28.7 1.0
O3P B:AMP602 2.2 29.3 1.0
O B:HOH675 2.3 36.8 1.0
CD B:GLU250 3.3 30.2 1.0
P B:AMP602 3.5 30.5 1.0
OE1 B:GLU250 3.7 25.9 1.0
MN B:MN506 3.9 39.4 1.0
O5' B:AMP602 4.0 36.0 1.0
OE1 B:GLU238 4.0 44.7 1.0
O2P B:AMP602 4.0 28.6 1.0
NH2 B:ARG249 4.0 28.2 1.0
N B:PHE236 4.0 31.5 1.0
O B:HOH678 4.1 46.7 1.0
O B:HOH679 4.1 50.7 1.0
O B:PHE236 4.2 34.7 1.0
O B:HOH680 4.3 39.6 1.0
O4' B:AMP602 4.3 48.4 1.0
OE2 B:GLU253 4.3 44.5 1.0
CG B:GLU250 4.6 32.6 1.0
OD2 B:ASP307 4.7 56.7 1.0
C B:GLY235 4.7 29.9 1.0
CB B:PHE236 4.7 32.3 1.0
CA B:GLY235 4.7 29.3 1.0
O1P B:AMP602 4.7 35.7 1.0
CA B:PHE236 4.7 32.1 1.0
NH1 B:ARG249 4.8 29.5 1.0
O B:HOH686 4.8 41.1 1.0
CZ B:ARG249 4.9 31.7 1.0
C4' B:AMP602 4.9 46.4 1.0
C B:PHE236 4.9 33.7 1.0

Manganese binding site 2 out of 9 in 2qjt

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Manganese binding site 2 out of 9 in the Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis


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 A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn506

b:39.4
occ:1.00
 O B:HOH687 1.9 45.6 1.0
OE1 B:GLU254 2.0 39.0 1.0
OE1 B:GLU250 2.2 25.9 1.0
O2P B:AMP602 2.4 28.6 1.0
O B:HOH686 2.5 41.1 1.0
OD2 B:ASP308 2.5 48.8 1.0
CD B:GLU254 3.1 38.0 1.0
MN B:MN507 3.2 36.0 1.0
CD B:GLU250 3.2 30.2 1.0
CG B:ASP308 3.4 49.2 1.0
OD2 B:ASP307 3.4 56.7 1.0
P B:AMP602 3.5 30.5 1.0
CG B:GLU254 3.5 38.7 1.0
OE2 B:GLU250 3.6 28.7 1.0
OD1 B:ASP308 3.7 49.6 1.0
O B:HOH680 3.8 39.6 1.0
O3P B:AMP602 3.8 29.3 1.0
O B:GLY234 3.8 29.8 1.0
O5' B:AMP602 3.8 36.0 1.0
MN B:MN505 3.9 34.7 1.0
OE2 B:GLU253 3.9 44.5 1.0
CG B:ASP307 4.2 52.3 1.0
OE2 B:GLU254 4.2 33.2 1.0
CB B:ASP307 4.4 50.5 1.0
CG B:GLU250 4.6 32.6 1.0
O B:HOH675 4.6 36.8 1.0
C B:GLY234 4.7 30.0 1.0
N B:ASP308 4.7 48.6 1.0
CA B:GLY235 4.7 29.3 1.0
O1P B:AMP602 4.8 35.7 1.0
CB B:ASP308 4.8 48.6 1.0
CB B:GLU250 4.9 34.1 1.0
O B:HOH685 5.0 30.0 1.0

Manganese binding site 3 out of 9 in 2qjt

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Manganese binding site 3 out of 9 in the Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis


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 A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn507

b:36.0
occ:1.00
 O2P B:AMP602 2.1 28.6 1.0
O B:GLY234 2.1 29.8 1.0
OD1 B:ASP308 2.2 49.6 1.0
O B:HOH685 2.2 30.0 1.0
O B:HOH684 2.3 28.6 1.0
OE1 B:GLU254 2.4 39.0 1.0
CG B:ASP308 3.2 49.2 1.0
CD B:GLU254 3.2 38.0 1.0
MN B:MN506 3.2 39.4 1.0
OE2 B:GLU254 3.3 33.2 1.0
C B:GLY234 3.4 30.0 1.0
P B:AMP602 3.4 30.5 1.0
OD2 B:ASP308 3.5 48.8 1.0
O1P B:AMP602 3.7 35.7 1.0
CA B:GLY235 4.0 29.3 1.0
N B:GLY235 4.1 30.2 1.0
O B:HOH681 4.1 37.4 1.0
NH1 B:ARG221 4.1 40.1 1.0
OE1 B:GLU250 4.2 25.9 1.0
O5' B:AMP602 4.2 36.0 1.0
O B:HOH682 4.3 49.3 1.0
N B:GLY234 4.4 32.6 1.0
CA B:GLY234 4.4 30.6 1.0
CB B:ASP308 4.5 48.6 1.0
O3P B:AMP602 4.6 29.3 1.0
CG B:GLU254 4.6 38.7 1.0
O B:HOH687 4.7 45.6 1.0
O B:HOH743 4.9 42.5 1.0

Manganese binding site 4 out of 9 in 2qjt

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Manganese binding site 4 out of 9 in the Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis


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 A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn509

b:89.7
occ:1.00
 NE2 B:HIS215 2.5 54.5 1.0
O B:HOH795 2.6 55.3 1.0
O B:HOH796 2.8 53.1 1.0
CE1 B:HIS215 3.4 55.5 1.0
CD2 B:HIS215 3.4 54.2 1.0
ND1 B:HIS215 4.5 56.1 1.0
CG B:HIS215 4.6 53.8 1.0
CB B:SER316 4.6 51.8 1.0
CD1 B:LEU300 4.8 52.8 1.0

Manganese binding site 5 out of 9 in 2qjt

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Manganese binding site 5 out of 9 in the Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis


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 A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:31.3
occ:1.00
 O2P A:AMP601 2.0 26.1 1.0
OE2 A:GLU254 2.1 30.8 1.0
O A:GLY234 2.1 23.6 1.0
O A:HOH693 2.2 29.8 1.0
O A:HOH694 2.2 24.0 1.0
OD1 A:ASP308 2.3 30.1 1.0
CD A:GLU254 3.1 29.1 1.0
CG A:ASP308 3.2 31.6 1.0
P A:AMP601 3.3 25.5 1.0
MN A:MN503 3.3 30.1 1.0
C A:GLY234 3.3 22.8 1.0
OE1 A:GLU254 3.4 28.5 1.0
OD2 A:ASP308 3.4 31.4 1.0
O1P A:AMP601 3.6 25.0 1.0
CA A:GLY235 4.0 22.3 1.0
O5' A:AMP601 4.0 29.4 1.0
O A:HOH695 4.0 30.6 1.0
N A:GLY235 4.1 23.3 1.0
O A:HOH696 4.2 41.6 1.0
NH1 A:ARG221 4.2 36.5 1.0
OE1 A:GLU250 4.3 24.6 1.0
N A:GLY234 4.3 22.6 1.0
O A:HOH720 4.4 42.9 1.0
CA A:GLY234 4.4 22.7 1.0
CG A:GLU254 4.4 26.1 1.0
O3P A:AMP601 4.5 18.4 1.0
CB A:ASP308 4.6 32.4 1.0
O A:HOH700 4.9 40.5 1.0

Manganese binding site 6 out of 9 in 2qjt

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Manganese binding site 6 out of 9 in the Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis


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 A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:52.8
occ:1.00
 OE1 A:GLN175 2.4 43.6 1.0
OE1 A:GLN178 2.5 51.0 1.0
O A:HOH679 2.6 41.5 1.0
NE2 A:GLN178 2.9 47.1 1.0
CD A:GLN178 3.0 46.4 1.0
CD A:GLN175 3.3 40.9 1.0
NE2 A:GLN175 3.6 33.7 1.0
CG A:GLN178 4.4 41.2 1.0
CG A:GLN175 4.6 39.6 1.0
CB A:GLN178 4.8 38.2 1.0
CA A:GLN175 4.9 40.1 1.0
CB A:GLN175 4.9 39.5 1.0

Manganese binding site 7 out of 9 in 2qjt

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Manganese binding site 7 out of 9 in the Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis


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 A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:30.1
occ:1.00
 OE2 A:GLU254 2.2 30.8 1.0
O A:HOH710 2.3 30.9 1.0
OE1 A:GLU250 2.3 24.6 1.0
O2P A:AMP601 2.4 26.1 1.0
OD2 A:ASP308 2.4 31.4 1.0
O A:HOH711 2.6 36.2 1.0
CD A:GLU254 3.2 29.1 1.0
MN A:MN501 3.3 31.3 1.0
CD A:GLU250 3.3 21.8 1.0
CG A:ASP308 3.4 31.6 1.0
CG A:GLU254 3.4 26.1 1.0
P A:AMP601 3.4 25.5 1.0
OE2 A:GLU250 3.7 25.4 1.0
O5' A:AMP601 3.7 29.4 1.0
OD1 A:ASP308 3.7 30.1 1.0
O3P A:AMP601 3.8 18.4 1.0
MN A:MN504 3.9 27.5 1.0
OE2 A:GLU253 4.0 33.5 1.0
O A:HOH790 4.0 43.9 1.0
O A:GLY234 4.1 23.6 1.0
OD2 A:ASP307 4.1 42.0 1.0
OE1 A:GLU254 4.3 28.5 1.0
CG A:ASP307 4.6 37.4 1.0
CG A:GLU250 4.6 25.7 1.0
O A:HOH794 4.7 31.1 1.0
CB A:ASP307 4.8 33.4 1.0
CB A:ASP308 4.8 32.4 1.0
O1P A:AMP601 4.8 25.0 1.0
O A:HOH704 4.8 26.6 1.0
C A:GLY234 4.8 22.8 1.0
CA A:GLY235 4.8 22.3 1.0
N A:ASP308 4.9 31.8 1.0
CB A:GLU254 4.9 27.6 1.0
CB A:GLU250 4.9 23.4 1.0
O A:HOH694 5.0 24.0 1.0

Manganese binding site 8 out of 9 in 2qjt

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Manganese binding site 8 out of 9 in the Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis


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 A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:27.5
occ:1.00
 O A:HOH711 1.7 36.2 1.0
O A:HOH703 2.2 31.5 1.0
O A:HOH704 2.2 26.6 1.0
O3P A:AMP601 2.2 18.4 1.0
OE2 A:GLU250 2.4 25.4 1.0
O A:HOH702 2.5 26.1 1.0
CD A:GLU250 3.4 21.8 1.0
P A:AMP601 3.5 25.5 1.0
OE1 A:GLU250 3.8 24.6 1.0
MN A:MN503 3.9 30.1 1.0
O2P A:AMP601 4.0 26.1 1.0
N A:PHE236 4.0 22.2 1.0
O5' A:AMP601 4.0 29.4 1.0
NH2 A:ARG249 4.0 20.2 1.0
O4' A:AMP601 4.2 31.9 1.0
O A:PHE236 4.3 22.6 1.0
O A:HOH794 4.3 31.1 1.0
OE2 A:GLU253 4.3 33.5 1.0
O A:HOH705 4.4 42.1 1.0
OE1 A:GLU238 4.4 38.5 1.0
O A:HOH701 4.5 42.8 1.0
O A:HOH790 4.5 43.9 1.0
O A:HOH712 4.6 36.9 1.0
O A:HOH710 4.6 30.9 1.0
NH1 A:ARG249 4.6 19.9 1.0
O1P A:AMP601 4.7 25.0 1.0
CA A:GLY235 4.7 22.3 1.0
CG A:GLU250 4.7 25.7 1.0
C A:GLY235 4.7 22.7 1.0
C4' A:AMP601 4.7 31.3 1.0
CB A:PHE236 4.8 21.9 1.0
CZ A:ARG249 4.8 20.6 1.0
CA A:PHE236 4.8 22.1 1.0
C5' A:AMP601 4.9 30.4 1.0
C A:PHE236 5.0 22.9 1.0

Manganese binding site 9 out of 9 in 2qjt

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Manganese binding site 9 out of 9 in the Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis


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 A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase Complexed with Amp and Mn Ion From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn508

b:66.3
occ:1.00
 O A:HOH783 2.1 41.0 1.0
NE2 A:HIS215 2.4 29.8 1.0
O A:HOH768 3.2 46.0 1.0
CD2 A:HIS215 3.3 25.4 1.0
CE1 A:HIS215 3.4 27.0 1.0
O A:HOH717 4.2 39.2 1.0
CG A:HIS215 4.5 29.4 1.0
ND1 A:HIS215 4.5 30.9 1.0
CB A:SER316 4.6 33.5 1.0
CD1 A:LEU300 4.7 27.4 1.0
OG A:SER316 4.8 34.8 1.0

Reference:

N.Huang, L.Sorci, X.Zhang, C.A.Brautigam, X.Li, N.Raffaelli, G.Magni, N.V.Grishin, A.L.Osterman, H.Zhang. Bifunctional Nmn Adenylyltransferase/Adp-Ribose Pyrophosphatase: Structure and Function in Bacterial Nad Metabolism. Structure V. 16 196 2008.
ISSN: ISSN 0969-2126
PubMed: 18275811
DOI: 10.1016/J.STR.2007.11.017
Page generated: Sat Oct 5 15:05:31 2024

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