Calcium in PDB 5v4d: Crystal Structure of the Protein of Unknown Function of the Conserved Rid Protein Family Yyfa From Yersinia Pestis

Protein crystallography data

The structure of Crystal Structure of the Protein of Unknown Function of the Conserved Rid Protein Family Yyfa From Yersinia Pestis, PDB code: 5v4d was solved by Y.Kim, G.Chhor, M.Endres, A.Krishnan, G.Babnigg, O.Schneewind, W.F.Anderson, A.Joachimiak, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.96 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.927, 80.919, 141.929, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 18

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Protein of Unknown Function of the Conserved Rid Protein Family Yyfa From Yersinia Pestis (pdb code 5v4d). 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 the Protein of Unknown Function of the Conserved Rid Protein Family Yyfa From Yersinia Pestis, PDB code: 5v4d:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5v4d

Go back to Calcium Binding Sites List in 5v4d
Calcium binding site 1 out of 6 in the Crystal Structure of the Protein of Unknown Function of the Conserved Rid Protein Family Yyfa From Yersinia Pestis


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 the Protein of Unknown Function of the Conserved Rid Protein Family Yyfa From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:18.4
occ:1.00
 O1 A:GOL203 2.3 25.5 1.0
OD1 A:ASP90 2.3 18.2 1.0
OD1 A:ASP94 2.4 18.8 1.0
O2 A:GOL203 2.4 37.3 1.0
O A:HOH314 2.4 25.1 1.0
O A:ASP90 2.5 17.2 1.0
CG A:ASP94 3.3 21.2 1.0
C2 A:GOL203 3.4 43.2 1.0
C1 A:GOL203 3.4 43.9 1.0
CG A:ASP90 3.4 16.0 1.0
C A:ASP90 3.5 15.9 1.0
OD2 A:ASP94 3.5 23.1 1.0
CA A:ASP90 3.9 14.5 1.0
O3 A:GOL203 4.1 52.6 1.0
C3 A:GOL203 4.1 42.9 1.0
CB A:ASP90 4.2 15.4 1.0
O A:HOH334 4.2 38.4 1.0
OD2 A:ASP90 4.3 22.2 1.0
O A:HOH309 4.4 27.0 1.0
O A:HOH325 4.5 42.4 1.0
N A:ILE91 4.6 14.7 1.0
CB A:ASP94 4.7 19.5 1.0
N A:ASP94 4.7 16.2 1.0
CB A:ALA93 4.9 13.9 1.0
O A:HOH398 4.9 29.9 1.0

Calcium binding site 2 out of 6 in 5v4d

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Calcium binding site 2 out of 6 in the Crystal Structure of the Protein of Unknown Function of the Conserved Rid Protein Family Yyfa From Yersinia Pestis


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 the Protein of Unknown Function of the Conserved Rid Protein Family Yyfa From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:14.8
occ:1.00
 O B:HOH326 2.3 17.3 1.0
O B:HOH408 2.4 20.5 1.0
O B:HOH360 2.4 15.9 1.0
O B:HOH394 2.4 15.7 1.0
OG F:SER110 2.4 15.2 1.0
OE1 B:GLU108 2.5 16.6 1.0
OE2 B:GLU108 2.5 16.2 1.0
CD B:GLU108 2.8 14.9 1.0
CB F:SER110 3.6 13.4 1.0
OG A:SER110 4.3 25.0 0.4
CA F:SER110 4.3 12.5 1.0
OE2 D:GLU108 4.3 19.0 1.0
CG B:GLU108 4.3 13.9 1.0
O D:HOH329 4.4 23.5 1.0
O F:SER110 4.4 15.7 1.0
O A:HOH391 4.4 20.5 1.0
O B:THR80 4.4 15.1 1.0
ND2 B:ASN81 4.5 13.2 1.0
O A:HOH303 4.6 29.8 1.0
N B:ILE82 4.7 15.7 1.0
C F:SER110 4.7 14.7 1.0
CA B:ASN81 4.7 14.9 1.0
O D:HOH384 4.8 39.7 1.0
CB A:ALA111 4.8 15.8 1.0
O B:HOH317 4.8 20.7 1.0
CB D:SER110 5.0 24.3 1.0

Calcium binding site 3 out of 6 in 5v4d

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Calcium binding site 3 out of 6 in the Crystal Structure of the Protein of Unknown Function of the Conserved Rid Protein Family Yyfa From Yersinia Pestis


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 the Protein of Unknown Function of the Conserved Rid Protein Family Yyfa From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:23.1
occ:1.00
 O B:HOH396 2.2 23.3 1.0
O B:VAL126 2.3 24.9 1.0
O B:HOH345 2.4 22.8 1.0
O B:GLY66 2.5 20.3 1.0
O B:HOH403 2.5 26.7 1.0
C B:VAL126 3.4 28.4 1.0
C B:GLY66 3.6 16.5 1.0
OXT B:VAL126 4.0 29.6 1.0
NZ B:LYS71 4.0 26.0 1.0
CA B:GLY66 4.4 17.2 1.0
CA B:VAL126 4.5 21.8 1.0
N B:THR67 4.5 15.8 1.0
CA B:THR67 4.5 15.4 1.0
O B:HOH401 4.6 23.0 1.0
CB B:VAL126 4.6 24.0 1.0
O B:ALA65 4.7 21.7 1.0
CB B:THR67 4.7 15.7 1.0
CG2 B:VAL126 4.9 23.1 1.0

Calcium binding site 4 out of 6 in 5v4d

Go back to Calcium Binding Sites List in 5v4d
Calcium binding site 4 out of 6 in the Crystal Structure of the Protein of Unknown Function of the Conserved Rid Protein Family Yyfa From Yersinia Pestis


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 the Protein of Unknown Function of the Conserved Rid Protein Family Yyfa From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca202

b:19.5
occ:1.00
 OD2 E:ASP94 2.4 19.8 1.0
O3 E:GOL204 2.4 24.8 1.0
OD1 E:ASP90 2.4 16.7 1.0
O E:HOH317 2.4 22.3 1.0
O2 E:GOL204 2.5 26.3 1.0
O E:ASP90 2.5 17.5 1.0
CG E:ASP94 3.3 19.7 1.0
C3 E:GOL204 3.4 35.8 1.0
C2 E:GOL204 3.4 34.7 1.0
CG E:ASP90 3.4 17.8 1.0
C E:ASP90 3.5 16.9 1.0
OD1 E:ASP94 3.5 25.5 1.0
C1 E:GOL204 4.0 36.6 1.0
CA E:ASP90 4.0 16.8 1.0
CB E:ASP90 4.2 15.0 1.0
O E:HOH323 4.3 23.7 1.0
OD2 E:ASP90 4.3 20.2 1.0
O E:HOH320 4.5 38.8 1.0
N E:ILE91 4.6 14.6 1.0
O1 E:GOL204 4.6 35.3 1.0
CB E:ASP94 4.6 15.6 1.0
N E:ASP94 4.7 15.9 1.0
CB E:ALA93 4.8 16.5 1.0
O E:HOH409 4.9 32.5 1.0

Calcium binding site 5 out of 6 in 5v4d

Go back to Calcium Binding Sites List in 5v4d
Calcium binding site 5 out of 6 in the Crystal Structure of the Protein of Unknown Function of the Conserved Rid Protein Family Yyfa From Yersinia Pestis


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 the Protein of Unknown Function of the Conserved Rid Protein Family Yyfa From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca203

b:16.4
occ:0.73
 O E:HOH356 2.3 39.0 1.0
O E:HOH363 2.4 43.4 1.0
O E:HOH394 2.4 36.0 1.0
O E:HOH337 2.6 34.4 1.0
O E:HOH414 3.7 51.8 1.0
OD2 E:ASP38 4.3 27.6 1.0
O E:HOH318 4.4 28.1 1.0
O E:HOH368 4.5 28.2 1.0
OD1 E:ASP38 4.6 28.7 1.0
OD1 E:ASN9 4.7 34.0 1.0
CG E:ASP38 4.9 24.0 1.0
O E:ASN9 4.9 22.1 1.0

Calcium binding site 6 out of 6 in 5v4d

Go back to Calcium Binding Sites List in 5v4d
Calcium binding site 6 out of 6 in the Crystal Structure of the Protein of Unknown Function of the Conserved Rid Protein Family Yyfa From Yersinia Pestis


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 the Protein of Unknown Function of the Conserved Rid Protein Family Yyfa From Yersinia Pestis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca202

b:15.5
occ:1.00
 O F:HOH327 2.4 15.8 1.0
O F:HOH401 2.4 19.9 1.0
O F:HOH341 2.4 16.9 1.0
O F:HOH395 2.4 16.9 1.0
OG B:SER110 2.5 15.4 1.0
OE2 F:GLU108 2.5 15.9 1.0
OE1 F:GLU108 2.5 16.9 1.0
CD F:GLU108 2.8 16.2 1.0
CB B:SER110 3.6 13.7 1.0
OG E:SER110 4.2 18.8 0.5
CA B:SER110 4.3 13.6 1.0
OE2 C:GLU108 4.3 22.3 1.0
CG F:GLU108 4.3 15.1 1.0
O C:HOH331 4.4 21.5 1.0
O A:HOH391 4.4 20.5 1.0
O E:HOH303 4.4 28.5 1.0
O F:THR80 4.4 16.0 1.0
O B:SER110 4.4 15.4 1.0
OD1 F:ASN81 4.5 15.4 1.0
C B:SER110 4.7 14.7 1.0
CA F:ASN81 4.8 14.0 1.0
N F:ILE82 4.8 14.4 1.0
O C:HOH390 4.8 40.6 1.0
CB C:SER110 4.9 22.4 1.0
O F:HOH312 4.9 21.2 1.0
CB E:ALA111 4.9 15.3 1.0
CG F:ASN81 5.0 16.1 1.0

Reference:

Y.Kim, G.Chhor, M.Endres, A.Krishnan, G.Babnigg, O.Schneewind, W.F.Anderson, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of the Protein of Unknown Function of the Conserved Rid Protein Family Yyfa From Yersinia Pestis To Be Published.
Page generated: Sat Dec 12 05:47:05 2020

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