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Magnesium in PDB 3ruv: Crystal Structure of Cpn-Rls in Complex with Atp Analogue From Methanococcus Maripaludis

Protein crystallography data

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

Resolution Low / High (Å) 48.81 / 2.24
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 161.019, 184.477, 184.785, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 22

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Cpn-Rls in Complex with Atp Analogue From Methanococcus Maripaludis (pdb code 3ruv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Cpn-Rls in Complex with Atp Analogue From Methanococcus Maripaludis, PDB code: 3ruv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3ruv

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Magnesium binding site 1 out of 8 in the Crystal Structure of Cpn-Rls in Complex with Atp Analogue 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-Rls in Complex with Atp Analogue From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg544

b:27.2
occ:1.00
 O1A A:ANP545 2.1 23.6 1.0
O A:HOH550 2.1 24.0 1.0
O A:HOH669 2.2 23.8 1.0
O3G A:ANP545 2.2 27.6 1.0
O1B A:ANP545 2.3 34.5 1.0
OD1 A:ASP91 2.3 30.4 1.0
CG A:ASP91 3.2 33.0 1.0
PB A:ANP545 3.3 23.2 1.0
OD2 A:ASP91 3.3 27.9 1.0
PA A:ANP545 3.4 24.9 1.0
PG A:ANP545 3.5 23.8 1.0
O3A A:ANP545 3.7 22.5 1.0
N3B A:ANP545 3.8 24.6 1.0
O A:HOH552 3.9 30.3 1.0
OD2 A:ASP386 4.1 31.4 1.0
O5' A:ANP545 4.1 31.3 1.0
O A:HOH567 4.2 24.8 1.0
O A:SER157 4.2 22.1 1.0
C5' A:ANP545 4.2 30.6 1.0
O1G A:ANP545 4.2 24.1 1.0
N A:GLY92 4.3 17.7 1.0
O2A A:ANP545 4.5 30.2 1.0
NZ A:LYS161 4.5 22.6 1.0
O A:HOH554 4.5 28.5 1.0
CA A:GLY160 4.5 19.3 1.0
CG A:ASP386 4.6 33.5 1.0
O2G A:ANP545 4.6 28.6 1.0
CB A:ASP91 4.6 26.6 1.0
O2B A:ANP545 4.6 24.3 1.0
C A:GLY160 4.8 30.5 1.0
OG A:SER157 4.9 25.7 1.0
CB A:ASP386 4.9 25.0 1.0

Magnesium binding site 2 out of 8 in 3ruv

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Magnesium binding site 2 out of 8 in the Crystal Structure of Cpn-Rls in Complex with Atp Analogue 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-Rls in Complex with Atp Analogue From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg549

b:42.2
occ:1.00
 O A:HOH561 2.1 20.9 1.0
O A:HOH560 2.2 33.5 1.0
O A:HOH563 2.2 27.3 1.0
OD1 A:ASP386 2.3 36.6 1.0
O A:HOH562 2.3 30.7 1.0
OD1 A:ASP60 2.3 25.8 1.0
CG A:ASP60 3.2 30.5 1.0
OD2 A:ASP60 3.4 28.0 1.0
CG A:ASP386 3.5 33.5 1.0
O A:GLY90 3.8 25.7 1.0
O A:HOH565 4.1 56.7 1.0
O A:HOH618 4.1 34.1 1.0
OD2 A:ASP386 4.2 31.4 1.0
NZ A:LYS161 4.3 22.6 1.0
O A:ARG382 4.3 25.8 1.0
O1G A:ANP545 4.4 24.1 1.0
CB A:ASP60 4.6 22.0 1.0
OE2 A:GLU86 4.7 42.1 1.0
CB A:ASP386 4.7 25.0 1.0
CA A:ASP386 4.7 29.8 1.0
N A:ASP386 4.8 28.5 1.0
CG1 A:VAL62 4.8 17.3 1.0
C A:GLY90 4.9 28.1 1.0
CG A:GLU86 4.9 33.1 1.0

Magnesium binding site 3 out of 8 in 3ruv

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Magnesium binding site 3 out of 8 in the Crystal Structure of Cpn-Rls in Complex with Atp Analogue 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-Rls in Complex with Atp Analogue From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg544

b:33.8
occ:1.00
 O3G B:ANP545 2.1 29.9 1.0
O1A B:ANP545 2.1 19.6 1.0
O B:HOH676 2.2 34.8 1.0
OD1 B:ASP91 2.3 29.0 1.0
O B:HOH631 2.3 29.2 1.0
O1B B:ANP545 2.3 26.0 1.0
CG B:ASP91 3.2 33.6 1.0
OD2 B:ASP91 3.3 33.6 1.0
PB B:ANP545 3.4 27.1 1.0
PG B:ANP545 3.4 30.2 1.0
PA B:ANP545 3.4 27.4 1.0
N3B B:ANP545 3.8 27.9 1.0
O3A B:ANP545 3.8 29.7 1.0
O B:HOH552 3.8 28.9 1.0
OD2 B:ASP386 4.1 36.8 1.0
O5' B:ANP545 4.2 40.4 1.0
O B:SER157 4.2 31.6 1.0
C5' B:ANP545 4.2 38.8 1.0
O1G B:ANP545 4.3 29.8 1.0
NZ B:LYS161 4.3 27.0 1.0
O B:HOH561 4.3 32.8 1.0
N B:GLY92 4.4 24.5 1.0
CA B:GLY160 4.5 29.9 1.0
O2G B:ANP545 4.5 35.8 1.0
CG B:ASP386 4.5 32.8 1.0
O2A B:ANP545 4.5 33.4 1.0
O B:HOH577 4.6 35.0 1.0
CB B:ASP91 4.6 21.3 1.0
O2B B:ANP545 4.7 26.7 1.0
C B:GLY160 4.8 31.7 1.0
CB B:ASP386 4.9 22.2 1.0
OG B:SER157 4.9 34.0 1.0
CG B:LYS161 5.0 39.8 1.0

Magnesium binding site 4 out of 8 in 3ruv

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Magnesium binding site 4 out of 8 in the Crystal Structure of Cpn-Rls in Complex with Atp Analogue 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-Rls in Complex with Atp Analogue From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg549

b:37.4
occ:1.00
 O B:HOH570 2.0 32.8 1.0
OD1 B:ASP386 2.2 34.2 1.0
O B:HOH567 2.2 31.5 1.0
O B:HOH569 2.3 33.6 1.0
O B:HOH568 2.3 34.6 1.0
OD1 B:ASP60 2.3 34.2 1.0
CG B:ASP60 3.2 36.1 1.0
CG B:ASP386 3.4 32.8 1.0
OD2 B:ASP60 3.5 32.3 1.0
O B:GLY90 3.8 37.2 1.0
OD2 B:ASP386 4.0 36.8 1.0
O B:HOH571 4.1 35.5 1.0
O B:ARG382 4.1 33.4 1.0
NZ B:LYS161 4.3 27.0 1.0
N B:ASP386 4.4 26.8 1.0
O1G B:ANP545 4.5 29.8 1.0
CB B:ASP386 4.5 22.2 1.0
CA B:ASP386 4.5 32.8 1.0
CB B:ASP60 4.5 27.0 1.0
OE1 B:GLU86 4.6 47.3 1.0
C B:GLY90 4.8 38.2 1.0
CE B:LYS161 5.0 32.4 1.0
C B:ARG382 5.0 33.6 1.0
CG1 B:VAL62 5.0 27.9 1.0

Magnesium binding site 5 out of 8 in 3ruv

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Magnesium binding site 5 out of 8 in the Crystal Structure of Cpn-Rls in Complex with Atp Analogue From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Cpn-Rls in Complex with Atp Analogue From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg544

b:30.2
occ:1.00
 O1B C:ANP545 2.1 22.7 1.0
O1A C:ANP545 2.2 21.6 1.0
O3G C:ANP545 2.2 28.1 1.0
O C:HOH553 2.2 29.6 1.0
O C:HOH551 2.3 27.3 1.0
OD1 C:ASP91 2.3 29.1 1.0
CG C:ASP91 3.1 32.9 1.0
PB C:ANP545 3.2 26.4 1.0
PG C:ANP545 3.3 24.4 1.0
OD2 C:ASP91 3.4 28.5 1.0
PA C:ANP545 3.4 27.4 1.0
O3A C:ANP545 3.7 23.4 1.0
N3B C:ANP545 3.7 26.9 1.0
O C:HOH550 3.9 23.6 1.0
O C:HOH554 4.0 22.9 1.0
N C:GLY92 4.1 20.1 1.0
OD2 C:ASP386 4.1 30.3 1.0
O1G C:ANP545 4.1 27.5 1.0
O5' C:ANP545 4.2 34.9 1.0
C5' C:ANP545 4.2 35.4 1.0
O C:SER157 4.3 27.3 1.0
O C:HOH557 4.5 26.4 1.0
O2B C:ANP545 4.5 24.7 1.0
O2G C:ANP545 4.5 34.8 1.0
CB C:ASP91 4.5 23.3 1.0
NZ C:LYS161 4.5 30.4 1.0
O2A C:ANP545 4.6 33.4 1.0
CG C:ASP386 4.6 33.2 1.0
CA C:GLY160 4.7 27.2 1.0
CA C:GLY92 4.8 17.0 1.0
CA C:ASP91 4.8 26.8 1.0
OG C:SER157 4.9 27.3 1.0
C C:ASP91 5.0 26.8 1.0

Magnesium binding site 6 out of 8 in 3ruv

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Magnesium binding site 6 out of 8 in the Crystal Structure of Cpn-Rls in Complex with Atp Analogue From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Cpn-Rls in Complex with Atp Analogue From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg549

b:38.7
occ:1.00
 OD1 C:ASP386 2.1 29.0 1.0
O C:HOH574 2.1 30.6 1.0
O C:HOH573 2.1 29.4 1.0
O C:HOH672 2.3 37.3 1.0
O C:HOH572 2.3 29.4 1.0
OD1 C:ASP60 2.4 23.9 1.0
CG C:ASP386 3.3 33.2 1.0
CG C:ASP60 3.4 27.2 1.0
O C:GLY90 3.6 33.3 1.0
OD2 C:ASP60 3.8 32.5 1.0
OD2 C:ASP386 4.0 30.3 1.0
O C:ARG382 4.0 29.2 1.0
NZ C:LYS161 4.2 30.4 1.0
N C:ASP386 4.4 22.7 1.0
O C:HOH576 4.4 44.7 1.0
O1G C:ANP545 4.4 27.5 1.0
CA C:ASP386 4.4 29.5 1.0
CB C:ASP386 4.4 21.2 1.0
O C:HOH687 4.5 46.1 1.0
CB C:ASP60 4.7 23.9 1.0
C C:GLY90 4.7 34.3 1.0
OE1 C:GLU86 4.9 47.1 1.0
O3G C:ANP545 4.9 28.1 1.0
CE C:LYS161 4.9 35.0 1.0
C C:ARG382 4.9 27.7 1.0

Magnesium binding site 7 out of 8 in 3ruv

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Magnesium binding site 7 out of 8 in the Crystal Structure of Cpn-Rls in Complex with Atp Analogue From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Cpn-Rls in Complex with Atp Analogue From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg544

b:39.6
occ:1.00
 O D:HOH638 2.2 26.8 1.0
O1A D:ANP545 2.2 28.1 1.0
O D:HOH639 2.2 33.2 1.0
O3G D:ANP545 2.2 28.9 1.0
O1B D:ANP545 2.2 33.5 1.0
OD1 D:ASP91 2.2 35.0 1.0
CG D:ASP91 3.1 36.2 1.0
OD2 D:ASP91 3.3 36.6 1.0
PB D:ANP545 3.3 31.1 1.0
PG D:ANP545 3.4 24.4 1.0
PA D:ANP545 3.4 32.1 1.0
O3A D:ANP545 3.7 35.4 1.0
N3B D:ANP545 3.7 23.6 1.0
O D:HOH550 3.9 32.7 1.0
OD2 D:ASP386 4.1 40.4 1.0
O D:HOH560 4.1 27.8 1.0
O5' D:ANP545 4.2 36.5 1.0
C5' D:ANP545 4.2 36.0 1.0
N D:GLY92 4.2 30.6 1.0
O1G D:ANP545 4.2 26.9 1.0
O D:SER157 4.3 30.0 1.0
O D:HOH575 4.4 35.2 1.0
CA D:GLY160 4.5 28.2 1.0
NZ D:LYS161 4.5 25.1 1.0
CB D:ASP91 4.5 25.7 1.0
O2A D:ANP545 4.6 35.1 1.0
O2G D:ANP545 4.6 32.6 1.0
CG D:ASP386 4.6 42.5 1.0
O2B D:ANP545 4.6 29.8 1.0
C D:GLY160 4.8 36.5 1.0
OG D:SER157 4.9 35.5 1.0
CA D:ASP91 4.9 28.1 1.0
CA D:GLY92 5.0 23.1 1.0

Magnesium binding site 8 out of 8 in 3ruv

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Magnesium binding site 8 out of 8 in the Crystal Structure of Cpn-Rls in Complex with Atp Analogue From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Cpn-Rls in Complex with Atp Analogue From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg549

b:42.8
occ:1.00
 O D:HOH577 2.1 35.7 1.0
O D:HOH579 2.2 33.3 1.0
O D:HOH580 2.3 34.8 1.0
O D:HOH578 2.3 37.1 1.0
OD1 D:ASP386 2.3 37.8 1.0
OD1 D:ASP60 2.4 24.4 1.0
CG D:ASP60 3.2 33.7 1.0
OD2 D:ASP60 3.5 32.1 1.0
CG D:ASP386 3.6 42.5 1.0
O D:GLY90 3.7 31.2 1.0
O D:HOH591 4.2 33.9 1.0
OD2 D:ASP386 4.2 40.4 1.0
O D:ARG382 4.3 35.1 1.0
O1G D:ANP545 4.3 26.9 1.0
NZ D:LYS161 4.4 25.1 1.0
N D:ASP386 4.6 31.2 1.0
OE2 D:GLU86 4.6 52.3 1.0
CB D:ASP60 4.6 25.4 1.0
CA D:ASP386 4.6 37.4 1.0
CB D:ASP386 4.7 32.2 1.0
OD2 D:ASP385 4.7 94.2 1.0
C D:GLY90 4.7 31.3 1.0
CG1 D:VAL62 4.9 24.7 1.0
CG D:GLU86 4.9 32.2 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: Thu Aug 15 10:39:40 2024

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