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Calcium in PDB 1kyt: Crystal Structure of Thermoplasma Acidophilum 0175 (APC014)

Protein crystallography data

The structure of Crystal Structure of Thermoplasma Acidophilum 0175 (APC014), PDB code: 1kyt was solved by Y.Kim, A.Joachimiak, A.Edwards, X.Xu, M.Pennycooke, J.Gu, F.Cheung, D.Christendat, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.14 / 1.70
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 88.526, 99.316, 113.886, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 24.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Thermoplasma Acidophilum 0175 (APC014) (pdb code 1kyt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Thermoplasma Acidophilum 0175 (APC014), PDB code: 1kyt:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1kyt

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Calcium binding site 1 out of 6 in the Crystal Structure of Thermoplasma Acidophilum 0175 (APC014)


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 Thermoplasma Acidophilum 0175 (APC014) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:17.0
occ:1.00
 OD1 A:ASN177 2.4 14.4 1.0
OD2 A:ASP178 2.4 12.1 1.0
OD1 A:ASP174 2.4 12.8 1.0
OD2 A:ASP8 2.6 13.9 1.0
O A:HOH534 2.6 17.3 1.0
O A:HOH567 2.7 22.7 1.0
CG A:ASP178 3.0 12.6 1.0
OD1 A:ASP178 3.0 13.9 1.0
OG A:SER175 3.2 15.4 1.0
CG A:ASN177 3.4 16.9 1.0
CG A:ASP8 3.6 13.7 1.0
CG A:ASP174 3.6 15.2 1.0
ND2 A:ASN177 3.8 9.5 1.0
O A:HOH570 3.9 18.4 1.0
N A:SER175 4.0 12.7 1.0
OD1 A:ASP8 4.1 11.4 1.0
OD2 A:ASP174 4.1 14.9 1.0
N A:ASP174 4.3 9.5 1.0
CB A:ASP178 4.4 10.7 1.0
CA A:GLY11 4.4 11.5 1.0
CB A:SER175 4.4 13.8 1.0
NZ A:LYS151 4.5 11.5 1.0
N A:ASP178 4.6 12.1 1.0
CB A:ASP8 4.6 12.7 1.0
CA A:SER175 4.7 11.3 1.0
N A:GLY11 4.8 11.0 1.0
C A:ASN177 4.8 13.1 1.0
CB A:ASN177 4.8 12.1 1.0
CB A:ASP174 4.8 10.4 1.0
C A:ASP174 4.8 8.4 1.0
CA A:ASP174 4.8 10.6 1.0
OG A:SER138 4.9 14.3 1.0
CA A:ASP178 4.9 8.5 1.0
O A:HOH659 5.0 26.6 1.0

Calcium binding site 2 out of 6 in 1kyt

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Calcium binding site 2 out of 6 in the Crystal Structure of Thermoplasma Acidophilum 0175 (APC014)


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 Thermoplasma Acidophilum 0175 (APC014) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:11.7
occ:1.00
 OD2 A:ASP174 2.4 14.9 1.0
O A:HOH538 2.5 11.0 1.0
O A:HOH514 2.5 11.2 1.0
O A:HOH524 2.6 16.1 1.0
O A:HOH532 2.6 10.7 1.0
O A:GLY11 2.6 9.8 1.0
O A:HOH530 2.6 13.6 1.0
C A:GLY11 3.5 10.1 1.0
CG A:ASP174 3.5 15.2 1.0
CA A:GLY11 3.6 11.5 1.0
CB A:ASP174 4.1 10.4 1.0
O A:HOH517 4.2 9.3 1.0
O A:HOH510 4.3 9.9 1.0
O A:HOH673 4.4 28.1 1.0
ND2 A:ASN193 4.4 13.4 1.0
O A:HOH570 4.4 18.4 1.0
O A:ASP10 4.4 10.9 1.0
O A:HOH568 4.5 19.1 1.0
OD1 A:ASP174 4.5 12.8 1.0
OD1 A:ASN193 4.6 13.4 1.0
O A:HOH525 4.6 11.3 1.0
N A:ASN12 4.7 8.1 1.0
N A:GLY11 4.9 11.0 1.0
CG A:ASN193 4.9 13.0 1.0

Calcium binding site 3 out of 6 in 1kyt

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Calcium binding site 3 out of 6 in the Crystal Structure of Thermoplasma Acidophilum 0175 (APC014)


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 Thermoplasma Acidophilum 0175 (APC014) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:17.3
occ:1.00
 O A:HOH537 3.1 13.1 1.0
O A:HOH508 3.1 11.2 1.0
O A:HOH554 3.2 16.0 1.0
N A:TYR140 3.3 8.8 1.0
O A:SER138 3.5 8.7 1.0
N A:ASN44 3.6 11.9 1.0
C A:GLY43 3.8 11.1 1.0
NE2 A:HIS143 3.9 13.9 1.0
CA A:ASN44 3.9 12.3 1.0
CA A:GLY139 3.9 8.9 1.0
CB A:ASN44 4.0 12.6 1.0
O A:GLY43 4.1 13.3 1.0
C A:GLY139 4.1 10.8 1.0
CB A:TYR140 4.2 11.4 1.0
CG A:ASN44 4.2 14.0 1.0
CE1 A:HIS143 4.2 10.6 1.0
ND2 A:ASN44 4.2 12.8 1.0
CD1 A:TYR140 4.2 10.4 1.0
CA A:TYR140 4.3 9.8 1.0
CA A:GLY43 4.3 11.0 1.0
C A:SER138 4.3 10.0 1.0
OD2 A:ASP10 4.5 24.2 1.0
OD1 A:ASP10 4.6 22.8 1.0
N A:GLY139 4.6 6.0 1.0
N A:GLY43 4.6 11.0 1.0
N A:SER141 4.6 9.1 1.0
CG A:ASP10 4.7 19.9 1.0
CG A:TYR140 4.7 9.2 1.0
OG A:SER42 4.7 15.6 1.0
OD1 A:ASN44 4.8 12.7 1.0
NH2 A:ARG108 4.8 10.7 1.0
C A:TYR140 4.9 11.2 1.0
OG A:SER141 4.9 13.9 1.0

Calcium binding site 4 out of 6 in 1kyt

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Calcium binding site 4 out of 6 in the Crystal Structure of Thermoplasma Acidophilum 0175 (APC014)


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 Thermoplasma Acidophilum 0175 (APC014) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:87.2
occ:1.00
 O A:HOH642 2.9 26.3 1.0
O A:HOH583 2.9 22.5 1.0
O A:HOH654 3.4 37.8 1.0
O A:VAL186 4.5 13.6 1.0
OD1 A:ASP203 4.6 19.0 1.0
OD2 A:ASP167 4.7 27.7 1.0
O A:PRO185 4.7 14.3 1.0
OD2 A:ASP203 4.8 16.6 1.0
O A:HOH610 4.8 35.5 1.0

Calcium binding site 5 out of 6 in 1kyt

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Calcium binding site 5 out of 6 in the Crystal Structure of Thermoplasma Acidophilum 0175 (APC014)


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 Thermoplasma Acidophilum 0175 (APC014) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:15.8
occ:1.00
 OD2 B:ASP8 2.4 12.5 1.0
O B:HOH508 2.5 14.3 1.0
OD1 B:ASP174 2.5 18.6 1.0
OD2 B:ASP178 2.6 15.1 1.0
O B:ASP10 2.6 16.9 1.0
O B:HOH510 2.6 13.9 1.0
OG B:SER175 2.6 14.9 1.0
CG B:ASP178 3.4 16.8 1.0
CG B:ASP8 3.4 13.3 1.0
OD1 B:ASP178 3.5 16.9 1.0
CG B:ASP174 3.6 18.1 1.0
C B:ASP10 3.7 16.5 1.0
CB B:SER175 3.8 14.9 1.0
ND2 B:ASN12 3.9 16.9 1.0
N B:SER175 3.9 18.3 1.0
OD1 B:ASP8 3.9 13.7 1.0
O B:HOH594 4.1 31.2 1.0
OD2 B:ASP174 4.1 19.1 1.0
ND2 B:ASN177 4.1 26.1 1.0
CB B:ASP10 4.4 16.4 1.0
N B:ASP174 4.4 14.4 1.0
CA B:SER175 4.5 18.7 1.0
CB B:ASP8 4.5 12.0 1.0
CA B:ASP10 4.5 15.3 1.0
O B:HOH605 4.5 29.5 1.0
OD2 B:ASP10 4.7 18.4 1.0
N B:GLY11 4.7 16.8 1.0
CA B:GLY11 4.7 16.8 1.0
C B:ASP174 4.8 16.0 1.0
CB B:ASP174 4.8 16.2 1.0
CB B:ASP178 4.8 17.1 1.0
N B:ASP10 4.9 14.8 1.0
CA B:ASP174 4.9 16.0 1.0
O B:HOH520 4.9 10.9 1.0

Calcium binding site 6 out of 6 in 1kyt

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Calcium binding site 6 out of 6 in the Crystal Structure of Thermoplasma Acidophilum 0175 (APC014)


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 Thermoplasma Acidophilum 0175 (APC014) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:46.3
occ:1.00
 O B:HOH634 2.6 21.5 1.0
O B:GLY139 2.6 19.8 1.0
O B:HOH633 2.6 20.6 1.0
O B:HOH635 3.0 38.2 1.0
O B:HOH505 3.0 36.5 1.0
O B:HOH531 3.2 33.0 1.0
C B:GLY139 3.6 20.0 1.0
CZ B:ARG18 3.7 52.2 1.0
NE B:ARG18 3.8 49.5 1.0
CA B:GLY139 3.9 16.4 1.0
NH2 B:ARG18 3.9 53.0 1.0
NH1 B:ARG18 4.1 53.0 1.0
N B:GLY139 4.3 16.0 1.0
CD B:ARG18 4.3 43.8 1.0
OD2 B:ASP10 4.5 18.4 1.0
CE1 B:TYR137 4.6 11.8 1.0
OD1 B:ASP10 4.6 19.5 1.0
OH B:TYR137 4.8 12.0 1.0
N B:TYR140 4.8 19.1 1.0
CG B:ASP10 4.9 18.1 1.0
CG B:ARG18 4.9 38.7 1.0

Reference:

Y.Kim, A.Joachimiak, A.Edwards, X.Xu, M.Pennycooke, J.Gu, F.Cheung, D.Christendat. Crystal Structure of Thermoplasma Acidophilum 0175 (APC014) To Be Published.
Page generated: Mon Jul 7 16:42:38 2025

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