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Calcium in PDB 6x95: 2-Deoxy-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain

Protein crystallography data

The structure of 2-Deoxy-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain, PDB code: 6x95 was solved by S.Guo, P.L.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.08 / 1.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.19, 50.03, 77.79, 90, 90, 90
R / Rfree (%) 15.6 / 16.9

Calcium Binding Sites:

The binding sites of Calcium atom in the 2-Deoxy-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain (pdb code 6x95). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the 2-Deoxy-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain, PDB code: 6x95:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 6x95

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Calcium binding site 1 out of 5 in the 2-Deoxy-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 2-Deoxy-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:7.3
occ:0.90
 OD1 A:ASP155 2.3 8.0 1.0
OD1 A:ASP110 2.3 8.1 1.0
O A:ASP159 2.4 9.0 1.0
O A:GLY157 2.4 8.8 1.0
OD2 A:ASP111 2.4 7.8 1.0
O4 A:Z61201 2.5 9.1 1.0
O3 A:Z61201 2.5 9.4 1.0
HO3 A:Z61201 3.1 11.4 1.0
HO4 A:Z61201 3.1 10.9 1.0
CG A:ASP110 3.3 8.2 1.0
C4 A:Z61201 3.3 9.8 1.0
CG A:ASP111 3.3 7.1 1.0
C3 A:Z61201 3.3 11.0 1.0
H A:GLY157 3.3 10.3 1.0
C A:GLY157 3.4 8.7 1.0
HG3 A:GLN156 3.5 11.2 1.0
H3 A:Z61201 3.5 13.2 1.0
CG A:ASP155 3.5 7.7 1.0
H4 A:Z61201 3.5 11.7 1.0
C A:ASP159 3.5 9.2 1.0
OD2 A:ASP110 3.6 9.4 1.0
H A:ASP159 3.7 11.5 0.6
H A:ASP159 3.7 11.5 0.4
OD1 A:ASP111 3.7 8.7 1.0
H A:GLN156 3.7 8.8 1.0
HE21 A:GLN156 3.7 13.8 1.0
HA A:ASP155 3.8 9.4 1.0
N A:ASP159 3.8 9.6 1.0
N A:GLY157 3.9 8.6 1.0
HA3 A:GLY158 4.0 12.1 1.0
C A:GLY158 4.2 8.9 1.0
HA A:TYR160 4.2 10.6 1.0
N A:GLN156 4.2 7.3 1.0
N A:GLY158 4.3 9.7 1.0
CA A:ASP159 4.3 9.2 0.4
CA A:ASP159 4.3 9.2 0.6
CA A:GLY157 4.3 9.6 1.0
OD2 A:ASP155 4.3 8.3 1.0
CA A:GLY158 4.4 10.0 1.0
N A:ASP111 4.4 7.3 1.0
CB A:ASP155 4.4 7.9 1.0
CA A:ASP155 4.4 7.8 1.0
C A:ASP110 4.4 7.9 1.0
HB2 A:ASP159 4.5 13.0 0.4
CG A:GLN156 4.5 9.3 1.0
H A:ASP111 4.5 8.8 1.0
HB3 A:TYR160 4.5 10.7 1.0
HB2 A:ASP155 4.5 9.6 1.0
NE2 A:GLN156 4.6 11.5 1.0
CB A:ASP110 4.6 8.8 1.0
CB A:ASP111 4.6 7.7 1.0
N A:TYR160 4.6 8.5 1.0
O A:ASP110 4.6 7.7 1.0
HB2 A:ASP159 4.7 12.7 0.6
C5 A:Z61201 4.7 13.7 1.0
HB2 A:ASP111 4.8 9.2 1.0
C A:ASP155 4.8 7.1 1.0
HB3 A:ASP110 4.8 10.6 1.0
C2 A:Z61201 4.8 12.6 1.0
HA A:ASP111 4.8 9.5 1.0
CA A:TYR160 4.8 8.8 1.0
H5 A:Z61201 4.8 16.4 1.0
C A:GLN156 4.8 8.1 1.0
HG2 A:GLN156 4.8 11.2 1.0
O A:GLY158 4.8 9.6 1.0
HA2 A:GLY157 4.9 11.5 1.0
O A:GLN129 4.9 10.4 1.0
CA A:ASP111 4.9 7.9 1.0
HD1 A:TYR160 5.0 10.3 1.0
CB A:ASP159 5.0 10.8 0.4
HA3 A:GLY157 5.0 11.5 1.0

Calcium binding site 2 out of 5 in 6x95

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Calcium binding site 2 out of 5 in the 2-Deoxy-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 2-Deoxy-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:8.6
occ:1.00
 O A:PRO82 2.3 9.5 1.0
O A:HOH343 2.4 11.4 1.0
O A:HOH415 2.4 10.2 1.0
O A:HOH406 2.4 8.6 1.0
O A:GLY64 2.4 9.4 1.0
O A:HOH405 2.4 9.9 1.0
OD1 A:ASP81 2.5 9.2 1.0
C A:GLY64 3.5 8.9 1.0
CG A:ASP81 3.5 8.4 1.0
C A:PRO82 3.5 8.7 1.0
HD2 A:PRO82 3.8 10.3 1.0
HE22 A:GLN68 3.8 10.5 1.0
OD2 A:ASP81 3.9 9.7 1.0
HA A:THR65 4.0 10.8 1.0
O A:HOH337 4.1 9.0 1.0
HA2 A:GLY83 4.1 12.8 1.0
HA2 A:GLY64 4.1 11.5 1.0
N A:PRO82 4.2 9.1 1.0
CA A:GLY64 4.2 9.6 1.0
HB2 A:PRO82 4.3 13.6 1.0
OE1 A:GLN68 4.4 9.0 1.0
C A:ASP81 4.4 9.2 1.0
CA A:PRO82 4.4 10.0 1.0
N A:GLY64 4.4 9.0 1.0
O A:GLY83 4.4 9.6 1.0
CD A:PRO82 4.5 8.6 1.0
H A:GLY64 4.5 10.8 0.5
H A:GLY64 4.5 10.8 0.5
N A:GLY83 4.5 9.6 1.0
C A:GLY83 4.5 8.9 1.0
N A:THR65 4.5 8.9 1.0
CA A:GLY83 4.5 10.6 1.0
NE2 A:GLN68 4.6 8.8 1.0
O A:ASP81 4.7 10.2 1.0
CA A:THR65 4.7 9.0 1.0
OD1 A:ASP84 4.8 11.1 1.0
HG22 A:THR65 4.8 13.0 1.0
CB A:ASP81 4.8 10.0 1.0
O A:HOH471 4.8 36.1 1.0
O A:HOH559 4.8 15.4 1.0
CB A:PRO82 4.8 11.3 1.0
HA A:ASP81 4.8 12.2 1.0
CD A:GLN68 4.9 7.7 1.0
CA A:ASP81 5.0 10.1 1.0
C A:LYS63 5.0 8.7 1.0
HA A:ASP84 5.0 12.3 1.0

Calcium binding site 3 out of 5 in 6x95

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Calcium binding site 3 out of 5 in the 2-Deoxy-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 2-Deoxy-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:8.5
occ:0.98
 OE1 A:GLN27 2.3 9.7 1.0
O A:GLN156 2.3 8.9 1.0
O A:HOH491 2.4 10.0 1.0
O A:HOH510 2.4 10.2 1.0
OD1 A:ASP87 2.4 8.5 1.0
O A:HOH365 2.4 12.9 1.0
OD2 A:ASP87 2.5 8.1 1.0
CG A:ASP87 2.8 8.2 1.0
HA A:GLN27 3.3 10.7 1.0
C A:GLN156 3.4 8.1 1.0
HB2 A:GLN156 3.5 10.4 1.0
CD A:GLN27 3.5 9.2 1.0
HA A:GLN156 3.7 9.4 1.0
HG1 A:THR86 3.8 10.9 1.0
OE1 A:GLN156 4.0 11.0 1.0
CA A:GLN156 4.0 7.8 1.0
H A:LEU28 4.0 9.7 1.0
HB2 A:GLN27 4.1 11.1 1.0
HE22 A:GLN27 4.1 12.0 1.0
CB A:GLN156 4.2 8.7 1.0
CA A:GLN27 4.2 8.9 1.0
NE2 A:GLN27 4.3 10.0 1.0
CB A:ASP87 4.3 8.9 1.0
HA3 A:GLY157 4.3 11.5 1.0
HB A:THR86 4.4 11.3 1.0
O A:HOH382 4.4 10.7 1.0
CD A:GLN156 4.4 10.9 1.0
O A:HOH550 4.5 30.2 1.0
CB A:GLN27 4.5 9.2 1.0
O A:HOH344 4.5 13.1 1.0
OG1 A:THR86 4.5 9.0 1.0
N A:GLY157 4.6 8.6 1.0
CG A:GLN27 4.6 10.0 1.0
O A:SER26 4.7 9.7 1.0
HB3 A:ASP87 4.7 10.7 1.0
N A:LEU28 4.7 8.0 1.0
HB2 A:ASP87 4.8 10.7 1.0
O A:THR86 4.8 8.8 1.0
HA A:ASP87 4.8 9.9 1.0
HB3 A:GLN156 4.9 10.4 1.0
CA A:GLY157 4.9 9.6 1.0
CG A:GLN156 4.9 9.3 1.0
CB A:THR86 4.9 9.4 1.0
N A:GLN27 5.0 8.6 1.0

Calcium binding site 4 out of 5 in 6x95

Go back to Calcium Binding Sites List in 6x95
Calcium binding site 4 out of 5 in the 2-Deoxy-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 2-Deoxy-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:13.4
occ:0.49
 O A:VAL38 2.3 11.8 1.0
O A:LYS41 2.4 11.4 1.0
O A:HOH512 2.4 21.0 1.0
O A:HOH520 2.4 23.9 1.0
O A:HOH504 2.5 23.7 1.0
OH A:TYR22 2.5 11.5 1.0
HE2 A:TYR22 3.1 12.4 1.0
CZ A:TYR22 3.5 9.8 1.0
C A:VAL38 3.5 10.7 1.0
C A:LYS41 3.5 11.5 1.0
HA A:GLU42 3.5 15.5 1.0
CE2 A:TYR22 3.6 10.3 1.0
H A:LYS41 3.6 13.9 1.0
HG13 A:VAL38 3.7 13.7 1.0
HA A:ASP39 3.8 15.9 1.0
HG12 A:VAL38 4.0 13.7 1.0
O A:HOH429 4.1 26.6 1.0
HA A:VAL38 4.2 11.8 1.0
CA A:GLU42 4.2 12.9 1.0
CG1 A:VAL38 4.3 11.4 1.0
N A:GLU42 4.3 12.3 1.0
H A:ALA43 4.3 13.0 1.0
N A:LYS41 4.3 11.6 1.0
O A:HOH463 4.3 19.3 1.0
O A:HOH446 4.4 31.0 1.0
CA A:VAL38 4.4 9.8 1.0
CA A:ASP39 4.4 13.2 1.0
N A:ASP39 4.4 11.6 1.0
O A:HOH327 4.5 35.8 1.0
N A:ALA43 4.5 10.8 1.0
C A:GLU42 4.6 11.2 1.0
CA A:LYS41 4.6 13.1 1.0
C A:ASP39 4.6 12.8 1.0
OE1 A:GLU20 4.7 14.3 1.0
CE1 A:TYR22 4.7 9.7 1.0
OE2 A:GLU42 4.9 38.2 1.0
CD2 A:TYR22 4.9 9.3 1.0
O A:ASP39 4.9 15.6 1.0
HE1 A:TYR22 5.0 11.7 1.0
N A:SER40 5.0 12.0 1.0

Calcium binding site 5 out of 5 in 6x95

Go back to Calcium Binding Sites List in 6x95
Calcium binding site 5 out of 5 in the 2-Deoxy-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of 2-Deoxy-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca206

b:11.2
occ:0.50
 OE1 A:GLU143 2.4 28.0 1.0
OE2 A:GLU143 2.4 22.9 1.0
O A:HOH511 2.5 30.1 1.0
O A:HOH496 2.5 34.8 1.0
O A:HOH508 2.6 29.5 1.0
CD A:GLU143 2.7 38.5 1.0
CG A:GLU143 4.2 24.8 1.0
O A:HOH529 4.5 32.3 1.0
HG2 A:GLU143 4.6 29.8 1.0
HG3 A:GLU143 4.7 29.8 1.0
HB2 A:GLU143 4.8 23.1 1.0
HB3 A:GLU143 4.8 23.1 1.0
O A:HOH372 4.8 18.5 1.0
CB A:GLU143 4.9 19.2 1.0

Reference:

S.Guo, T.D.R.Vance, H.Zahiri, R.Eves, C.Stevens, J.H.Hehemann, S.Vidal-Melgosa, P.L.Davies. Structural Basis of Ligand Selectivity By A Bacterial Adhesin Lectin Involved in Multispecies Biofilm Formation. Mbio V. 12 2021.
ISSN: ESSN 2150-7511
PubMed: 33824212
DOI: 10.1128/MBIO.00130-21
Page generated: Tue Jul 16 17:56:01 2024

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