Atomistry » Magnesium » PDB 3rr5-3rv4 » 3ruq
Atomistry »
  Magnesium »
    PDB 3rr5-3rv4 »
      3ruq »

Magnesium in PDB 3ruq: Crystal Structure of Cpn-Wt in Complex with Adp From Methanococcus Maripaludis

Protein crystallography data

The structure of Crystal Structure of Cpn-Wt in Complex with Adp From Methanococcus Maripaludis, PDB code: 3ruq was solved by J.H.Pereira, C.Y.Ralston, N.R.Douglas, R.Kumar, R.P.Mcandrew, K.M.Knee, J.Frydman, P.D.Adams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.90 / 2.80
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 162.164, 185.002, 184.769, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 21.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Cpn-Wt in Complex with Adp From Methanococcus Maripaludis (pdb code 3ruq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Cpn-Wt in Complex with Adp From Methanococcus Maripaludis, PDB code: 3ruq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3ruq

Go back to Magnesium Binding Sites List in 3ruq
Magnesium binding site 1 out of 4 in the Crystal Structure of Cpn-Wt in Complex with Adp From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Cpn-Wt in Complex with Adp From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg544

b:32.5
occ:1.00
O A:HOH546 2.0 40.6 1.0
OD1 A:ASP91 2.1 69.3 1.0
O2A A:ADP545 2.2 45.8 1.0
O A:HOH559 2.2 49.6 1.0
O3B A:ADP545 2.3 45.4 1.0
CG A:ASP91 2.8 64.0 1.0
OD2 A:ASP91 2.9 62.8 1.0
PB A:ADP545 3.5 32.3 1.0
PA A:ADP545 3.5 35.6 1.0
O A:HOH560 3.5 54.4 1.0
O3A A:ADP545 3.9 46.8 1.0
O1B A:ADP545 4.0 37.0 1.0
O A:SER157 4.2 40.8 1.0
N A:GLY92 4.2 38.8 1.0
C5' A:ADP545 4.2 45.9 1.0
O5' A:ADP545 4.2 44.7 1.0
NZ A:LYS161 4.3 65.9 1.0
CB A:ASP91 4.3 47.9 1.0
CE A:LYS161 4.4 54.5 1.0
OD2 A:ASP386 4.6 78.1 1.0
O A:HOH561 4.7 61.0 1.0
OG A:SER157 4.7 51.8 1.0
O1A A:ADP545 4.7 44.6 1.0
O2B A:ADP545 4.8 38.9 1.0
CA A:ASP91 4.9 38.5 1.0
CA A:SER157 4.9 36.6 1.0
CA A:GLY92 4.9 39.8 1.0
CG A:ASP386 5.0 94.8 1.0
C A:SER157 5.0 44.7 1.0

Magnesium binding site 2 out of 4 in 3ruq

Go back to Magnesium Binding Sites List in 3ruq
Magnesium binding site 2 out of 4 in the Crystal Structure of Cpn-Wt in Complex with Adp From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Cpn-Wt in Complex with Adp From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg544

b:33.1
occ:1.00
OD1 B:ASP91 2.1 57.4 1.0
O3B B:ADP545 2.2 53.2 1.0
O2A B:ADP545 2.3 38.4 1.0
O B:HOH555 2.3 59.0 1.0
O B:HOH546 2.5 34.8 1.0
O B:HOH554 2.7 57.5 1.0
CG B:ASP91 2.8 56.0 1.0
OD2 B:ASP91 2.8 56.7 1.0
PB B:ADP545 3.4 44.6 1.0
PA B:ADP545 3.6 43.6 1.0
O1B B:ADP545 3.7 38.4 1.0
O3A B:ADP545 3.8 51.1 1.0
N B:GLY92 4.1 47.1 1.0
C5' B:ADP545 4.1 51.9 1.0
CB B:ASP91 4.2 44.5 1.0
O B:SER157 4.2 41.1 1.0
O5' B:ADP545 4.3 43.5 1.0
NZ B:LYS161 4.3 77.7 1.0
O B:HOH547 4.4 47.6 1.0
CE B:LYS161 4.5 69.5 1.0
OD2 B:ASP386 4.6 85.1 1.0
O2B B:ADP545 4.7 39.9 1.0
CA B:ASP91 4.8 34.5 1.0
OG B:SER157 4.8 56.9 1.0
O1A B:ADP545 4.8 47.3 1.0
CA B:GLY92 4.8 44.8 1.0
C B:ASP91 4.9 41.0 1.0
CA B:SER157 5.0 34.8 1.0
CG B:ASP386 5.0 0.0 1.0

Magnesium binding site 3 out of 4 in 3ruq

Go back to Magnesium Binding Sites List in 3ruq
Magnesium binding site 3 out of 4 in the Crystal Structure of Cpn-Wt in Complex with Adp From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Cpn-Wt in Complex with Adp From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg544

b:40.5
occ:1.00
OD1 C:ASP91 2.1 50.9 1.0
O C:HOH558 2.2 48.8 1.0
O2A C:ADP545 2.2 42.4 1.0
O C:HOH546 2.2 46.2 1.0
O C:HOH559 2.6 34.9 1.0
O3B C:ADP545 2.6 39.1 1.0
CG C:ASP91 3.1 48.0 1.0
OD2 C:ASP91 3.3 60.7 1.0
PB C:ADP545 3.4 36.2 1.0
PA C:ADP545 3.5 37.4 1.0
O1B C:ADP545 3.6 41.8 1.0
OD2 C:ASP386 3.7 86.2 1.0
O3A C:ADP545 3.8 49.8 1.0
CE C:LYS161 4.0 64.4 1.0
NZ C:LYS161 4.1 52.8 1.0
O C:HOH547 4.2 48.8 1.0
N C:GLY92 4.3 34.4 1.0
CG C:ASP386 4.3 98.4 1.0
O C:SER157 4.4 40.6 1.0
CB C:ASP91 4.5 26.8 1.0
O5' C:ADP545 4.6 51.2 1.0
O1A C:ADP545 4.6 48.9 1.0
O C:HOH560 4.6 59.6 1.0
CB C:ASP386 4.7 94.3 1.0
C5' C:ADP545 4.7 49.0 1.0
CA C:ASP91 4.8 31.2 1.0
O2B C:ADP545 4.9 45.0 1.0
OG C:SER157 4.9 54.7 1.0

Magnesium binding site 4 out of 4 in 3ruq

Go back to Magnesium Binding Sites List in 3ruq
Magnesium binding site 4 out of 4 in the Crystal Structure of Cpn-Wt in Complex with Adp From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Cpn-Wt in Complex with Adp From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg544

b:44.7
occ:1.00
O2A D:ADP545 2.0 49.2 1.0
O D:HOH553 2.1 61.9 1.0
O D:HOH546 2.2 44.2 1.0
O D:HOH554 2.2 62.3 1.0
OD1 D:ASP91 2.2 59.5 1.0
O1B D:ADP545 2.4 42.5 1.0
CG D:ASP91 3.1 55.3 1.0
OD2 D:ASP91 3.2 53.0 1.0
PA D:ADP545 3.4 34.3 1.0
PB D:ADP545 3.4 43.9 1.0
O3B D:ADP545 3.7 44.4 1.0
O3A D:ADP545 3.7 0.3 1.0
CE D:LYS161 4.1 55.1 1.0
NZ D:LYS161 4.1 59.7 1.0
N D:GLY92 4.2 41.9 1.0
OD2 D:ASP386 4.3 95.2 1.0
C5' D:ADP545 4.3 50.3 1.0
O D:SER157 4.3 46.2 1.0
O D:HOH547 4.3 37.4 1.0
O5' D:ADP545 4.4 58.6 1.0
O1A D:ADP545 4.4 49.1 1.0
CB D:ASP91 4.5 42.1 1.0
CG D:ASP386 4.8 99.7 1.0
O2B D:ADP545 4.8 48.2 1.0
O D:HOH555 4.9 53.8 1.0
CA D:ASP91 4.9 36.6 1.0
OG D:SER157 4.9 58.1 1.0
CA D:GLY92 5.0 43.6 1.0

Reference:

J.H.Pereira, C.Y.Ralston, N.R.Douglas, R.Kumar, T.Lopez, R.P.Mcandrew, K.M.Knee, J.A.King, J.Frydman, P.D.Adams. Mechanism of Nucleotide Sensing in Group II Chaperonins. Embo J. V. 31 731 2012.
ISSN: ISSN 0261-4189
PubMed: 22193720
DOI: 10.1038/EMBOJ.2011.468
Page generated: Mon Dec 14 08:46:21 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy