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Calcium in PDB 2gq4: Crystal Structure of An Rna Racemate

Protein crystallography data

The structure of Crystal Structure of An Rna Racemate, PDB code: 2gq4 was solved by W.Rypniewski, M.Vallazza, M.Perbandt, S.Klussmann, C.Betzel, V.A.Erdmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.35
Space group P -1
Cell size a, b, c (Å), α, β, γ (°) 26.933, 38.160, 45.897, 112.25, 101.56, 92.20
R / Rfree (%) n/a / 27

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of An Rna Racemate (pdb code 2gq4). 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 An Rna Racemate, PDB code: 2gq4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2gq4

Go back to Calcium Binding Sites List in 2gq4
Calcium binding site 1 out of 6 in the Crystal Structure of An Rna Racemate


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 An Rna Racemate within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca310

b:22.9
occ:0.40
 O M:HOH49 2.3 32.6 0.5
O L:HOH74 2.5 39.1 0.5
O L:HOH88 2.5 36.9 0.5
O M:HOH87 2.5 32.5 0.5
O L:HOH110 2.5 41.9 0.5
O L:HOH102 2.5 37.5 0.5
O2' L:0G97 2.5 17.1 0.5
O3' L:0G97 2.6 18.9 0.5
C2' L:0G97 3.4 16.3 0.5
C3' L:0G97 3.5 17.5 0.5
C4' L:0G97 4.1 17.1 0.5
OP2 M:0G82 4.6 19.9 0.5
OP1 M:0G83 4.6 20.3 0.5
C1' L:0G97 4.8 15.9 0.5

Calcium binding site 2 out of 6 in 2gq4

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Calcium binding site 2 out of 6 in the Crystal Structure of An Rna Racemate


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 An Rna Racemate within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca308

b:25.6
occ:0.50
 O M:HOH30 2.3 29.5 0.5
O M:HOH104 2.3 42.0 0.5
O M:HOH73 2.4 35.3 0.5
O M:HOH44 2.5 38.4 0.5
O3' M:0G86 2.5 21.2 0.5
O M:HOH27 2.5 29.9 0.5
O2' M:0G86 2.5 21.8 0.5
O M:HOH35 2.6 32.4 0.5
C2' M:0G86 3.4 19.5 0.5
C3' M:0G86 3.4 19.4 0.5
C4' M:0G86 4.1 19.0 0.5
C1' M:0G86 4.8 18.9 0.5
O4' M:0G86 5.0 19.7 0.5

Calcium binding site 3 out of 6 in 2gq4

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Calcium binding site 3 out of 6 in the Crystal Structure of An Rna Racemate


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 An Rna Racemate within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca311

b:23.9
occ:0.35
 O M:HOH1 2.4 16.4 0.5
O M:HOH53 2.5 31.6 0.5
O M:HOH246 2.5 43.0 0.5
O M:HOH21 2.6 26.4 0.5
N7 M:0G82 2.6 16.6 0.5
O M:HOH77 3.4 47.5 0.5
O6 M:0G82 3.6 17.5 0.5
C5 M:0G82 3.6 14.4 0.5
C8 M:0G82 3.6 16.4 0.5
C6 M:0G82 4.0 16.8 0.5
O N:HOH64 4.2 33.5 0.5
O M:HOH160 4.3 44.4 0.5
O M:HOH227 4.3 57.8 0.5
N7 M:0G81 4.4 16.3 0.5
OP1 M:0G82 4.4 20.1 0.5
O M:HOH109 4.5 45.7 0.5
O N:HOH12 4.7 26.0 0.5
O6 M:0G83 4.7 17.5 0.5
N7 M:0G83 4.7 17.9 0.5
C5 M:0G81 4.8 16.1 0.5
N9 M:0G82 4.8 16.2 0.5
C4 M:0G82 4.8 15.5 0.5
C8 M:0G81 4.9 16.9 0.5
OP1 M:0G81 4.9 22.1 0.5

Calcium binding site 4 out of 6 in 2gq4

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Calcium binding site 4 out of 6 in the Crystal Structure of An Rna Racemate


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 An Rna Racemate within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Ca302

b:27.3
occ:0.35
 O N:HOH98 2.1 36.0 0.5
O N:HOH26 2.4 30.8 0.5
O N:HOH5 2.4 23.1 0.5
O N:HOH80 2.4 36.3 0.5
O N:HOH101 2.5 39.5 0.5
O N:HOH6 2.6 20.1 0.5
CA N:CA304 2.8 31.0 0.3
O N:HOH56 2.8 33.3 0.5
O N:HOH250 3.9 49.0 0.5
O6 N:0G97 4.3 16.3 0.5
O N:HOH135 4.3 44.7 0.5
O N:HOH205 4.4 65.2 0.5
O N:HOH38 4.5 32.5 0.5
N7 N:0G96 4.6 15.6 0.5
O4 N:0U95 4.8 18.5 0.5
O N:HOH167 4.8 51.0 0.5
OP1 N:0G96 4.9 20.6 0.5
N7 N:0G97 5.0 15.7 0.5

Calcium binding site 5 out of 6 in 2gq4

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Calcium binding site 5 out of 6 in the Crystal Structure of An Rna Racemate


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 An Rna Racemate within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Ca304

b:31.0
occ:0.35
 O N:HOH38 2.2 32.5 0.5
O N:HOH5 2.3 23.1 0.5
O N:HOH26 2.4 30.8 0.5
OP1 N:0G96 2.4 20.6 0.5
O N:HOH144 2.8 48.8 0.5
CA N:CA302 2.8 27.3 0.3
O N:HOH56 2.8 33.3 0.5
O N:HOH167 3.1 51.0 0.5
O N:HOH250 3.4 49.0 0.5
P N:0G96 3.8 19.1 0.5
O5' N:0G96 4.2 16.9 0.5
O N:HOH98 4.3 36.0 0.5
N7 N:0G96 4.4 15.6 0.5
O N:HOH149 4.6 38.0 0.5
C8 N:0G96 4.6 16.5 0.5
OP2 N:0G96 4.6 21.6 0.5
O N:HOH6 4.7 20.1 0.5
O N:HOH80 4.7 36.3 0.5
O N:HOH101 4.7 39.5 0.5
O N:HOH124 4.8 39.0 0.5
OP1 N:0G97 4.8 20.0 0.5
N7 N:0G97 4.9 15.7 0.5
O3' N:0U95 5.0 16.7 0.5

Calcium binding site 6 out of 6 in 2gq4

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Calcium binding site 6 out of 6 in the Crystal Structure of An Rna Racemate


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 An Rna Racemate within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Ca306

b:21.1
occ:0.40
 O K:HOH33 2.3 30.4 0.5
O N:HOH100 2.4 40.9 0.5
O K:HOH51 2.4 29.6 0.5
O3' N:0G97 2.5 19.2 0.5
O N:HOH87 2.5 37.7 0.5
O N:HOH61 2.5 35.7 0.5
O2' N:0G97 2.5 17.8 0.5
O N:HOH54 2.6 35.4 0.5
C2' N:0G97 3.4 16.4 0.5
C3' N:0G97 3.5 16.2 0.5
C4' N:0G97 4.1 16.5 0.5
OP2 K:0G82 4.7 16.4 0.5
OP1 K:0G83 4.7 14.7 0.5
OP2 K:0G83 4.7 15.2 0.5
C1' N:0G97 4.8 16.2 0.5

Reference:

W.Rypniewski, M.Vallazza, M.Perbandt, S.Klussmann, L.J.Delucas, C.Betzel, V.A.Erdmann. The First Crystal Structure of An Rna Racemate. Acta Crystallogr.,Sect.D V. 62 659 2006.
ISSN: ISSN 0907-4449
PubMed: 16699193
DOI: 10.1107/S090744490601359X
Page generated: Fri Jul 12 10:51:26 2024

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