Atomistry » Calcium » PDB 2fod-2g81 » 2g32
Atomistry »
  Calcium »
    PDB 2fod-2g81 »
      2g32 »

Calcium in PDB 2g32: Crystal Structure of An Rna Racemate

Protein crystallography data

The structure of Crystal Structure of An Rna Racemate, PDB code: 2g32 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) 20.00 / 1.30
Space group P -1
Cell size a, b, c (Å), α, β, γ (°) 26.263, 37.724, 45.117, 112.86, 100.72, 93.04
R / Rfree (%) 23.9 / 25.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of An Rna Racemate (pdb code 2g32). 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: 2g32:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2g32

Go back to Calcium Binding Sites List in 2g32
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:23.5
occ:0.40
 O M:HOH74 2.2 34.2 0.5
O L:HOH223 2.3 44.9 0.5
O L:HOH56 2.3 35.7 0.5
O L:HOH98 2.4 37.4 0.5
O L:HOH104 2.4 39.3 0.5
O M:HOH110 2.4 37.8 0.5
O2' L:0G97 2.5 15.8 0.5
O3' L:0G97 2.5 17.8 0.5
C2' L:0G97 3.4 16.1 0.5
C3' L:0G97 3.4 16.4 0.5
C4' L:0G97 4.0 16.4 0.5
OP2 M:0G82 4.5 20.0 0.5
OP1 M:0G83 4.5 18.9 0.5
C1' L:0G97 4.7 15.4 0.5
C5' L:0G97 4.9 16.0 0.5
O L:HOH141 4.9 39.7 0.5
O4' L:0G97 4.9 16.1 0.5

Calcium binding site 2 out of 6 in 2g32

Go back to Calcium Binding Sites List in 2g32
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:24.3
occ:0.50
 O M:HOH60 2.3 29.8 0.5
O M:HOH121 2.4 36.3 0.5
O M:HOH44 2.4 31.5 0.5
O3' M:0G86 2.4 19.9 0.5
O M:HOH87 2.4 35.1 0.5
O M:HOH30 2.5 30.2 0.5
O M:HOH45 2.5 27.9 0.5
O2' M:0G86 2.5 20.8 0.5
C2' M:0G86 3.4 18.1 0.5
C3' M:0G86 3.4 17.9 0.5
C4' M:0G86 4.0 18.0 0.5
C1' M:0G86 4.7 18.0 0.5
O4' M:0G86 4.9 18.4 0.5

Calcium binding site 3 out of 6 in 2g32

Go back to Calcium Binding Sites List in 2g32
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:23.7
occ:0.25
 O M:HOH193 2.1 42.8 0.5
O M:HOH7 2.3 17.4 0.5
O M:HOH103 2.5 35.0 0.5
N7 M:0G82 2.6 17.6 0.5
O M:HOH37 2.6 28.8 0.5
O6 M:0G82 3.4 18.0 0.5
C5 M:0G82 3.5 15.5 0.5
C8 M:0G82 3.6 16.3 0.5
O M:HOH116 3.7 42.8 0.5
C6 M:0G82 3.9 18.0 0.5
O N:HOH126 4.0 34.7 0.5
O M:HOH91 4.1 46.4 0.5
O M:HOH187 4.2 47.1 0.5
N7 M:0G81 4.3 16.6 0.5
OP1 M:0G82 4.4 19.7 0.5
O M:HOH251 4.5 43.0 0.5
O N:HOH249 4.5 49.8 0.5
O6 M:0G83 4.6 18.5 0.5
N7 M:0G83 4.6 18.3 0.5
C5 M:0G81 4.7 17.0 0.5
C4 M:0G82 4.7 15.6 0.5
N9 M:0G82 4.7 16.0 0.5
O N:HOH25 4.8 25.9 0.5
C8 M:0G81 4.8 16.4 0.5
OP1 M:0G81 4.9 23.5 0.5
O6 M:0G81 5.0 16.5 0.5

Calcium binding site 4 out of 6 in 2g32

Go back to Calcium Binding Sites List in 2g32
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:24.9
occ:0.40
 O N:HOH8 2.3 19.1 0.5
O N:HOH34 2.3 27.8 0.5
O N:HOH108 2.3 34.5 0.5
O N:HOH21 2.3 25.9 0.5
O N:HOH257 2.4 46.0 0.5
O N:HOH6 2.4 18.5 0.5
O N:HOH125 2.5 32.4 0.5
O N:HOH18 2.6 26.9 0.5
CA N:CA304 2.8 27.2 0.3
O6 N:0G97 4.2 15.7 0.5
O N:HOH130 4.3 36.1 0.5
O N:HOH122 4.3 38.3 0.5
O N:HOH31 4.4 25.1 0.5
N7 N:0G96 4.5 15.0 0.5
O N:HOH145 4.6 43.6 0.5
O4 N:0U95 4.8 18.3 0.5
OP1 N:0G96 4.8 19.2 0.5
N7 N:0G97 4.9 14.9 0.5
O6 N:0G96 5.0 16.9 0.5

Calcium binding site 5 out of 6 in 2g32

Go back to Calcium Binding Sites List in 2g32
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:27.2
occ:0.30
 O N:HOH31 2.1 25.1 0.5
OP1 N:0G96 2.3 19.2 0.5
O N:HOH8 2.4 19.1 0.5
O N:HOH21 2.4 25.9 0.5
O N:HOH145 2.5 43.6 0.5
O N:HOH18 2.6 26.9 0.5
O N:HOH122 2.7 38.3 0.5
CA N:CA302 2.8 24.9 0.4
O N:HOH257 2.9 46.0 0.5
P N:0G96 3.7 17.6 0.5
O5' N:0G96 4.2 15.7 0.5
N7 N:0G96 4.3 15.0 0.5
O N:HOH34 4.4 27.8 0.5
C8 N:0G96 4.5 15.8 0.5
O N:HOH108 4.5 34.5 0.5
OP2 N:0G96 4.5 19.9 0.5
O N:HOH6 4.6 18.5 0.5
OP1 N:0G97 4.7 18.8 0.5
O N:HOH125 4.7 32.4 0.5
N7 N:0G97 4.8 14.9 0.5
O N:HOH70 4.8 29.8 0.5
O3' N:0U95 4.9 15.3 0.5
C3' N:0U95 5.0 14.1 0.5

Calcium binding site 6 out of 6 in 2g32

Go back to Calcium Binding Sites List in 2g32
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:0.45
 O K:HOH41 2.3 27.4 0.5
O N:HOH48 2.4 32.8 0.5
O N:HOH99 2.4 35.4 0.5
O N:HOH43 2.4 30.8 0.5
O N:HOH39 2.4 27.0 0.5
O N:HOH63 2.5 30.3 0.5
O3' N:0G97 2.5 18.1 0.5
O2' N:0G97 2.5 17.8 0.5
C2' N:0G97 3.4 16.4 0.5
C3' N:0G97 3.4 16.6 0.5
C4' N:0G97 4.0 16.2 0.5
O N:HOH210 4.5 46.4 0.5
OP2 K:0G82 4.7 15.1 0.5
O N:HOH32 4.7 27.9 0.5
C1' N:0G97 4.7 15.7 0.5
OP1 K:0G83 4.8 15.6 0.5
O4' N:0G97 5.0 15.7 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 10:40:59 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy