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Calcium in PDB 3pk0: Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis

Protein crystallography data

The structure of Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis, PDB code: 3pk0 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) 41.23 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.140, 78.010, 155.430, 90.00, 102.22, 90.00
R / Rfree (%) 15 / 18.3

Other elements in 3pk0:

The structure of Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis (pdb code 3pk0). 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 Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis, PDB code: 3pk0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3pk0

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Calcium binding site 1 out of 8 in the Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis


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 Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca270

b:26.2
occ:0.50
 CA A:CA270 0.0 26.2 0.5
CA A:CA270 1.5 24.1 0.5
OD1 A:ASP97 2.2 18.2 1.0
O A:HOH598 2.4 33.5 1.0
O A:HOH291 2.5 10.0 1.0
CG A:ASP97 3.2 17.8 1.0
OD2 A:ASP97 3.5 18.7 1.0
N A:ASP97 4.5 13.5 1.0
CB A:ASP97 4.5 13.7 1.0
O A:HOH341 4.6 13.5 1.0

Calcium binding site 2 out of 8 in 3pk0

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Calcium binding site 2 out of 8 in the Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis


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 Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca270

b:24.1
occ:0.50
 CA A:CA270 0.0 24.1 0.5
CA A:CA270 1.5 26.2 0.5
OD1 A:ASP97 2.4 18.2 1.0
O A:HOH598 3.2 33.5 1.0
CG A:ASP97 3.6 17.8 1.0
O A:HOH291 3.6 10.0 1.0
N A:ASP97 4.1 13.5 1.0
OD2 A:ASP97 4.2 18.7 1.0
O A:ASP97 4.4 12.8 1.0
CB A:ASP97 4.8 13.7 1.0
CA A:PRO96 4.9 15.4 1.0
CA A:ASP97 4.9 13.5 1.0
O A:HOH341 5.0 13.5 1.0

Calcium binding site 3 out of 8 in 3pk0

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Calcium binding site 3 out of 8 in the Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis


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 Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca280

b:37.3
occ:1.00
 OD1 A:ASP51 2.3 27.7 1.0
O A:HOH319 2.3 8.9 1.0
O A:ASP51 2.3 26.2 1.0
O A:GLY54 2.4 21.6 1.0
O A:GLY56 2.4 22.9 1.0
O A:HOH283 2.4 6.4 1.0
C A:ASP51 3.3 25.8 1.0
CG A:ASP51 3.4 31.6 1.0
C A:GLY54 3.5 21.2 1.0
C A:GLY56 3.6 22.6 1.0
CA A:ASP51 3.6 25.7 1.0
N A:GLY56 4.0 20.7 1.0
C A:SER55 4.1 21.1 1.0
CB A:ASP51 4.1 26.8 1.0
CA A:GLY56 4.3 21.2 1.0
N A:GLY54 4.3 21.6 1.0
N A:SER55 4.4 21.0 1.0
OD2 A:ASP51 4.4 39.2 1.0
CA A:SER55 4.4 21.3 1.0
O A:HOH266 4.5 7.3 1.0
O A:SER55 4.5 21.4 1.0
CA A:GLY54 4.5 21.1 1.0
N A:GLN52 4.5 25.5 1.0
CG2 A:VAL58 4.5 20.6 1.0
O A:LEU50 4.6 21.0 1.0
N A:LYS57 4.6 22.6 1.0
CA A:LYS57 4.8 23.1 1.0
O A:HOH490 4.9 22.8 1.0
N A:ASP51 4.9 23.6 1.0
N A:VAL58 5.0 22.2 1.0

Calcium binding site 4 out of 8 in 3pk0

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Calcium binding site 4 out of 8 in the Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis


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 Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca270

b:17.9
occ:0.50
 CA B:CA270 0.0 17.9 0.5
CA B:CA270 1.5 32.8 0.5
O B:HOH331 2.1 18.8 1.0
O B:HOH772 2.3 37.3 1.0
OD1 B:ASP97 2.4 18.0 1.0
CG B:ASP97 3.6 17.4 1.0
O B:HOH291 3.8 4.2 1.0
OD2 B:ASP97 4.2 17.9 1.0
N B:ASP97 4.2 12.6 1.0
O B:ASP97 4.4 13.0 1.0
CB B:ASP97 4.8 13.2 1.0
CA B:ASP97 4.9 12.1 1.0
O B:HOH277 5.0 11.2 1.0
CA B:PRO96 5.0 15.5 1.0

Calcium binding site 5 out of 8 in 3pk0

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Calcium binding site 5 out of 8 in the Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis


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 Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca270

b:32.8
occ:0.50
 CA B:CA270 0.0 32.8 0.5
CA B:CA270 1.5 17.9 0.5
OD1 B:ASP97 2.2 18.0 1.0
O B:HOH772 2.4 37.3 1.0
O B:HOH291 2.6 4.2 1.0
CG B:ASP97 3.1 17.4 1.0
O B:HOH331 3.2 18.8 1.0
OD2 B:ASP97 3.4 17.9 1.0
CB B:ASP97 4.5 13.2 1.0
N B:ASP97 4.6 12.6 1.0
O B:HOH277 4.7 11.2 1.0
O B:ASP97 5.0 13.0 1.0

Calcium binding site 6 out of 8 in 3pk0

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Calcium binding site 6 out of 8 in the Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis


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 Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca280

b:47.5
occ:1.00
 O B:GLY56 2.4 24.7 1.0
O B:ASP51 2.4 28.7 1.0
O B:GLY54 2.5 27.9 1.0
O B:HOH319 2.5 7.9 1.0
O B:HOH431 2.5 20.0 1.0
OD1 B:ASP51 2.7 34.8 1.0
C B:ASP51 3.4 28.5 1.0
C B:GLY54 3.6 26.9 1.0
CG B:ASP51 3.6 32.8 1.0
C B:GLY56 3.6 24.9 1.0
CA B:ASP51 3.7 28.1 1.0
N B:GLY56 4.0 25.6 1.0
C B:SER55 4.1 27.0 1.0
CB B:ASP51 4.2 29.4 1.0
N B:GLY54 4.3 26.4 1.0
N B:SER55 4.4 26.6 1.0
CA B:GLY56 4.4 24.4 1.0
O B:HOH281 4.4 7.7 1.0
O B:SER55 4.5 28.6 1.0
OD2 B:ASP51 4.5 37.5 1.0
CA B:SER55 4.5 27.9 1.0
CA B:GLY54 4.5 26.3 1.0
N B:LYS57 4.6 24.8 1.0
N B:GLN52 4.6 28.8 1.0
O B:LEU50 4.6 24.3 1.0
CG2 B:VAL58 4.7 23.1 1.0
CA B:LYS57 4.7 25.2 1.0
N B:VAL58 4.8 23.8 1.0
N B:ASP51 4.9 26.1 1.0

Calcium binding site 7 out of 8 in 3pk0

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Calcium binding site 7 out of 8 in the Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis


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 Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca280

b:50.2
occ:1.00
 O C:ASP51 2.3 32.1 1.0
O C:HOH532 2.4 25.9 1.0
O C:GLY54 2.4 29.2 1.0
O C:HOH311 2.4 11.6 1.0
O C:GLY56 2.5 27.9 1.0
OD1 C:ASP51 2.7 37.2 1.0
C C:ASP51 3.2 31.6 1.0
C C:GLY54 3.5 28.5 1.0
CA C:ASP51 3.6 31.3 1.0
CG C:ASP51 3.6 36.1 1.0
C C:GLY56 3.6 26.8 1.0
N C:GLY56 3.9 26.7 1.0
C C:SER55 4.1 28.7 1.0
CB C:ASP51 4.2 32.5 1.0
N C:SER55 4.3 28.5 1.0
N C:GLY54 4.3 28.0 1.0
CA C:SER55 4.4 29.4 1.0
CA C:GLY56 4.4 26.3 1.0
O C:HOH268 4.4 10.9 1.0
N C:GLN52 4.4 32.2 1.0
OD2 C:ASP51 4.5 39.7 1.0
CA C:GLY54 4.5 27.6 1.0
O C:LEU50 4.6 25.9 1.0
O C:SER55 4.6 28.5 1.0
N C:LYS57 4.7 26.9 1.0
CA C:LYS57 4.8 27.3 1.0
CG2 C:VAL58 4.8 26.2 1.0
N C:ASP51 4.8 29.5 1.0
CA C:GLN52 5.0 34.0 1.0

Calcium binding site 8 out of 8 in 3pk0

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Calcium binding site 8 out of 8 in the Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis


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 Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca280

b:19.3
occ:1.00
 OD1 D:ASP51 2.3 22.8 1.0
O D:GLY56 2.3 20.1 1.0
O D:ASP51 2.4 20.9 1.0
O D:GLY54 2.4 20.3 1.0
O D:HOH315 2.4 4.3 1.0
C D:ASP51 3.3 20.7 1.0
CG D:ASP51 3.4 21.9 1.0
C D:GLY54 3.5 20.4 1.0
C D:GLY56 3.6 20.8 1.0
CA D:ASP51 3.7 20.4 1.0
N D:GLY56 4.1 19.8 1.0
CB D:ASP51 4.1 21.6 1.0
C D:SER55 4.2 21.1 1.0
N D:SER55 4.3 20.4 1.0
N D:GLY54 4.3 20.6 1.0
OD2 D:ASP51 4.4 25.6 1.0
CA D:SER55 4.4 21.5 1.0
CA D:GLY56 4.4 19.3 1.0
O D:HOH260 4.4 6.3 1.0
CA D:GLY54 4.5 20.0 1.0
N D:LYS57 4.5 20.8 1.0
N D:GLN52 4.6 20.6 1.0
CA D:LYS57 4.6 22.4 1.0
O D:SER55 4.7 20.5 1.0
O D:LEU50 4.8 18.8 1.0
N D:VAL58 4.8 21.8 1.0
CG2 D:VAL58 4.8 18.6 1.0
O D:HOH688 5.0 37.1 1.0

Reference:

L.Baugh, I.Phan, D.W.Begley, M.C.Clifton, B.Armour, D.M.Dranow, B.M.Taylor, M.M.Muruthi, J.Abendroth, J.W.Fairman, D.Fox, S.H.Dieterich, B.L.Staker, A.S.Gardberg, R.Choi, S.N.Hewitt, A.J.Napuli, J.Myers, L.K.Barrett, Y.Zhang, M.Ferrell, E.Mundt, K.Thompkins, N.Tran, S.Lyons-Abbott, A.Abramov, A.Sekar, D.Serbzhinskiy, D.Lorimer, G.W.Buchko, R.Stacy, L.J.Stewart, T.E.Edwards, W.C.Van Voorhis, P.J.Myler. Increasing the Structural Coverage of Tuberculosis Drug Targets. Tuberculosis (Edinb) V. 95 142 2015.
ISSN: ISSN 1472-9792
PubMed: 25613812
DOI: 10.1016/J.TUBE.2014.12.003
Page generated: Sat Jul 13 16:50:20 2024

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