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Calcium in PDB 3s55: Crystal Structure of A Putative Short-Chain Dehydrogenase/Reductase From Mycobacterium Abscessus Bound to Nad

Protein crystallography data

The structure of Crystal Structure of A Putative Short-Chain Dehydrogenase/Reductase From Mycobacterium Abscessus Bound to Nad, PDB code: 3s55 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 69.360, 84.970, 100.890, 81.77, 76.78, 74.23
R / Rfree (%) 18.9 / 23.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Putative Short-Chain Dehydrogenase/Reductase From Mycobacterium Abscessus Bound to Nad (pdb code 3s55). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of A Putative Short-Chain Dehydrogenase/Reductase From Mycobacterium Abscessus Bound to Nad, PDB code: 3s55:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3s55

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Calcium binding site 1 out of 8 in the Crystal Structure of A Putative Short-Chain Dehydrogenase/Reductase From Mycobacterium Abscessus Bound to Nad


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Putative Short-Chain Dehydrogenase/Reductase From Mycobacterium Abscessus Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca280

b:22.9
occ:1.00
 O A:HOH923 2.2 15.7 1.0
O A:HOH924 2.4 9.1 1.0
O A:HOH925 2.5 9.7 1.0
O A:HOH926 2.6 18.5 1.0
OE2 A:GLU6 2.6 17.8 1.0
OE1 A:GLU6 2.6 19.9 1.0
CD A:GLU6 3.0 20.1 1.0
CG A:GLU6 4.5 18.3 1.0
N A:ALA3 4.6 30.3 1.0

Calcium binding site 2 out of 8 in 3s55

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Calcium binding site 2 out of 8 in the Crystal Structure of A Putative Short-Chain Dehydrogenase/Reductase From Mycobacterium Abscessus Bound to Nad


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Putative Short-Chain Dehydrogenase/Reductase From Mycobacterium Abscessus Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca280

b:25.8
occ:1.00
 O E:HOH962 2.2 14.2 1.0
O B:HOH961 2.4 20.1 1.0
O B:GLY96 2.5 14.5 1.0
O B:HOH845 2.6 16.9 1.0
OD2 B:ASP98 2.7 12.5 1.0
OD1 B:ASP98 2.7 17.5 1.0
O E:HOH455 2.9 20.3 1.0
CG B:ASP98 3.0 13.2 1.0
C B:GLY96 3.4 14.7 1.0
N B:GLY96 3.9 16.3 1.0
CA B:GLY96 3.9 15.5 1.0
O B:HOH408 4.2 10.2 1.0
O B:GLY7 4.3 16.0 1.0
O E:HOH602 4.4 11.5 1.0
O B:HOH631 4.4 17.4 1.0
OE2 E:GLU257 4.4 17.3 1.0
C B:GLY95 4.4 16.7 1.0
CB B:ASP98 4.5 11.5 1.0
N B:ILE97 4.5 13.7 1.0
N B:THR9 4.6 8.7 1.0
OE1 E:GLU257 4.6 22.2 1.0
CB B:THR9 4.6 8.3 1.0
OG1 B:THR9 4.7 9.0 1.0
N B:ASP98 4.7 11.3 1.0
O E:HOH688 4.7 20.8 1.0
CD B:ARG145 4.8 5.4 1.0
NE B:ARG145 4.9 7.7 1.0
C B:ILE97 4.9 11.9 1.0
O B:GLY95 4.9 16.9 1.0
CD E:GLU257 5.0 16.8 1.0
CA B:LYS8 5.0 12.1 1.0
CA B:ILE97 5.0 12.6 1.0

Calcium binding site 3 out of 8 in 3s55

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Calcium binding site 3 out of 8 in the Crystal Structure of A Putative Short-Chain Dehydrogenase/Reductase From Mycobacterium Abscessus Bound to Nad


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Putative Short-Chain Dehydrogenase/Reductase From Mycobacterium Abscessus Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca281

b:30.3
occ:1.00
 OE2 B:GLU6 2.2 17.6 1.0
O B:HOH964 2.4 17.4 1.0
O B:HOH966 2.8 13.4 1.0
O E:HOH823 2.9 18.5 1.0
CD B:GLU6 3.1 17.6 1.0
OE1 B:GLU6 3.4 18.2 1.0
O B:HOH965 3.4 22.7 1.0
O E:GLY31 4.0 11.5 1.0
OD2 E:ASP33 4.3 12.1 1.0
OD1 E:ASP33 4.4 8.9 1.0
N E:GLY7 4.5 15.9 1.0
CG B:GLU6 4.5 16.1 1.0
CG E:ASP33 4.7 10.8 1.0

Calcium binding site 4 out of 8 in 3s55

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Calcium binding site 4 out of 8 in the Crystal Structure of A Putative Short-Chain Dehydrogenase/Reductase From Mycobacterium Abscessus Bound to Nad


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of A Putative Short-Chain Dehydrogenase/Reductase From Mycobacterium Abscessus Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca280

b:36.7
occ:1.00
 OE1 D:GLU58 2.4 12.2 1.0
OE2 D:GLU58 2.4 10.3 1.0
O D:HOH1059 2.4 5.0 1.0
OD1 D:ASP55 2.6 8.2 1.0
CD D:GLU58 2.7 12.1 1.0
CG D:ASP55 3.8 10.5 1.0
CG D:GLU58 4.2 9.7 1.0
CA D:ASP55 4.3 10.2 1.0
N D:ASP55 4.5 11.3 1.0
CB D:ASP55 4.6 9.8 1.0
OD2 D:ASP55 4.7 10.3 1.0
NH2 D:ARG21 4.8 11.8 1.0
O D:ASP54 4.9 13.2 1.0
C D:ASP54 4.9 12.6 1.0

Calcium binding site 5 out of 8 in 3s55

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Calcium binding site 5 out of 8 in the Crystal Structure of A Putative Short-Chain Dehydrogenase/Reductase From Mycobacterium Abscessus Bound to Nad


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of A Putative Short-Chain Dehydrogenase/Reductase From Mycobacterium Abscessus Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca280

b:29.4
occ:1.00
 O E:HOH980 2.3 22.6 1.0
O B:HOH812 2.4 10.4 1.0
O B:HOH978 2.4 21.7 1.0
OE2 E:GLU6 2.4 23.3 1.0
O B:HOH902 2.5 18.5 1.0
OE1 E:GLU6 2.6 21.1 1.0
CD E:GLU6 2.9 22.6 1.0
O B:HOH979 3.0 22.4 1.0
NE B:ARG68 4.3 22.7 1.0
O B:GLY31 4.3 9.1 1.0
CG E:GLU6 4.4 21.0 1.0
OD1 B:ASP33 4.4 14.5 1.0
CD B:ARG68 4.6 17.1 1.0
OD2 B:ASP33 4.6 14.7 1.0
O B:HOH435 4.6 16.9 1.0
N B:GLY7 4.7 14.3 1.0
O B:HOH786 4.7 9.8 1.0
CG B:ASP33 4.8 12.8 1.0

Calcium binding site 6 out of 8 in 3s55

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Calcium binding site 6 out of 8 in the Crystal Structure of A Putative Short-Chain Dehydrogenase/Reductase From Mycobacterium Abscessus Bound to Nad


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of A Putative Short-Chain Dehydrogenase/Reductase From Mycobacterium Abscessus Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca280

b:25.2
occ:1.00
 O F:HOH1109 2.4 11.0 1.0
O F:HOH1106 2.4 15.0 1.0
O F:HOH1105 2.4 13.6 1.0
O F:HOH1108 2.4 27.2 1.0
OE2 F:GLU6 2.4 19.8 1.0
O F:HOH1107 2.6 18.4 1.0
OE1 F:GLU6 2.8 20.3 1.0
CD F:GLU6 3.0 18.9 1.0
CG F:GLU6 4.5 18.3 1.0
OD2 F:ASP4 4.9 30.6 1.0

Calcium binding site 7 out of 8 in 3s55

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Calcium binding site 7 out of 8 in the Crystal Structure of A Putative Short-Chain Dehydrogenase/Reductase From Mycobacterium Abscessus Bound to Nad


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of A Putative Short-Chain Dehydrogenase/Reductase From Mycobacterium Abscessus Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca281

b:25.3
occ:1.00
 O F:HOH722 2.4 20.5 1.0
O F:GLY96 2.4 14.2 1.0
O F:HOH1243 2.5 18.3 1.0
OD2 F:ASP98 2.8 9.8 1.0
OD1 F:ASP98 2.8 13.4 1.0
CG F:ASP98 3.1 11.8 1.0
C F:GLY96 3.4 14.4 1.0
N F:GLY96 3.8 16.2 1.0
CA F:GLY96 3.8 15.8 1.0
O F:GLY7 4.3 16.6 1.0
C F:GLY95 4.5 17.4 1.0
N F:ILE97 4.5 13.8 1.0
O F:HOH1131 4.5 8.5 1.0
N F:THR9 4.6 11.5 1.0
O F:HOH323 4.6 7.5 1.0
CB F:ASP98 4.6 10.1 1.0
OG1 F:THR9 4.7 14.9 1.0
CD F:ARG145 4.7 9.4 1.0
N F:ASP98 4.7 10.3 1.0
NE F:ARG145 4.8 11.6 1.0
C F:ILE97 4.8 11.3 1.0
O F:GLY95 4.9 17.6 1.0
CA F:ILE97 5.0 12.5 1.0
CB F:THR9 5.0 11.0 1.0

Calcium binding site 8 out of 8 in 3s55

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Calcium binding site 8 out of 8 in the Crystal Structure of A Putative Short-Chain Dehydrogenase/Reductase From Mycobacterium Abscessus Bound to Nad


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of A Putative Short-Chain Dehydrogenase/Reductase From Mycobacterium Abscessus Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca280

b:35.1
occ:1.00
 OE1 H:GLU58 2.4 11.2 1.0
O H:HOH765 2.5 13.8 1.0
O H:HOH708 2.5 10.2 1.0
OD1 H:ASP55 2.6 7.9 1.0
OE2 H:GLU58 2.8 13.2 1.0
CD H:GLU58 2.9 11.8 1.0
CG H:ASP55 3.9 10.2 1.0
CG H:GLU58 4.4 8.6 1.0
CA H:ASP55 4.5 9.1 1.0
N H:ASP55 4.7 9.3 1.0
OD2 H:ASP55 4.8 12.9 1.0
O H:HOH678 4.8 18.0 1.0
CB H:ASP55 4.8 9.5 1.0

Reference:

D.H.Haft, P.G.Pierce, S.J.Mayclin, A.Sullivan, A.S.Gardberg, J.Abendroth, D.W.Begley, I.Q.Phan, B.L.Staker, P.J.Myler, V.M.Marathias, D.D.Lorimer, T.E.Edwards. Mycofactocin-Associated Mycobacterial Dehydrogenases with Non-Exchangeable Nad Cofactors. Sci Rep V. 7 41074 2017.
ISSN: ESSN 2045-2322
PubMed: 28120876
DOI: 10.1038/SREP41074
Page generated: Tue Jul 8 16:29:55 2025

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