Atomistry » Magnesium » PDB 4kfu-4knw » 4ki8
Atomistry »
  Magnesium »
    PDB 4kfu-4knw »
      4ki8 »

Magnesium in PDB 4ki8: Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State

Protein crystallography data

The structure of Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State, PDB code: 4ki8 was solved by X.Fei, D.Yang, N.Laronde-Leblanc, G.H.Lorimer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.17 / 2.72
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 235.222, 141.655, 156.693, 90.00, 113.84, 90.00
R / Rfree (%) 16.6 / 20.3

Other elements in 4ki8:

The structure of Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State also contains other interesting chemical elements:

Potassium (K) 9 atoms
Calcium (Ca) 11 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State (pdb code 4ki8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State, PDB code: 4ki8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4ki8

Go back to Magnesium Binding Sites List in 4ki8
Magnesium binding site 1 out of 7 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State


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 A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:33.9
occ:1.00
 O A:HOH716 2.0 44.5 1.0
O A:HOH710 2.1 32.8 1.0
O A:HOH750 2.1 48.5 1.0
O3B A:ADP601 2.2 49.5 1.0
OD1 A:ASP87 2.2 72.9 1.0
OD2 A:ASP87 2.3 63.8 1.0
O2A A:ADP601 2.4 39.7 1.0
CG A:ASP87 2.6 66.5 1.0
PB A:ADP601 3.3 57.0 1.0
O1B A:ADP601 3.4 58.3 1.0
PA A:ADP601 3.7 51.8 1.0
O3A A:ADP601 3.9 75.2 1.0
O A:HOH711 4.0 43.6 1.0
CB A:ASP87 4.1 56.7 1.0
C5' A:ADP601 4.2 56.1 1.0
O A:HOH749 4.4 68.6 1.0
O A:HOH770 4.4 61.2 1.0
O5' A:ADP601 4.4 55.7 1.0
N A:GLY88 4.5 43.8 1.0
O2B A:ADP601 4.6 59.9 1.0
O A:HOH745 4.6 57.9 1.0
O A:SER151 4.7 85.2 1.0
CA A:SER151 4.8 64.3 1.0
CA A:ASP87 4.9 39.9 1.0
O1A A:ADP601 4.9 60.9 1.0

Magnesium binding site 2 out of 7 in 4ki8

Go back to Magnesium Binding Sites List in 4ki8
Magnesium binding site 2 out of 7 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State


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 A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:29.0
occ:1.00
 O B:HOH757 2.0 44.0 1.0
O B:HOH753 2.1 43.7 1.0
OD2 B:ASP87 2.2 46.4 1.0
O2B B:ADP601 2.2 52.9 1.0
OD1 B:ASP87 2.2 74.1 1.0
O2A B:ADP601 2.5 30.3 1.0
CG B:ASP87 2.5 48.6 1.0
O B:HOH758 2.8 51.2 1.0
PB B:ADP601 3.4 45.9 1.0
O3B B:ADP601 3.5 45.1 1.0
O B:HOH711 3.6 57.9 1.0
PA B:ADP601 3.8 43.0 1.0
O B:HOH761 3.9 63.4 1.0
O3A B:ADP601 4.0 0.6 1.0
CB B:ASP87 4.1 32.3 1.0
C5' B:ADP601 4.2 46.0 1.0
O5' B:ADP601 4.5 46.3 1.0
O B:HOH766 4.6 47.2 0.8
O1B B:ADP601 4.6 47.7 1.0
N B:GLY88 4.6 28.5 1.0
O B:HOH717 4.7 49.1 1.0
O B:HOH799 4.9 38.5 0.6
O B:SER151 4.9 89.9 1.0
CA B:ASP87 4.9 27.7 1.0
CA B:SER151 4.9 57.8 1.0

Magnesium binding site 3 out of 7 in 4ki8

Go back to Magnesium Binding Sites List in 4ki8
Magnesium binding site 3 out of 7 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State


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 A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:34.9
occ:1.00
 O C:HOH781 2.1 92.1 1.0
O C:HOH749 2.1 72.8 1.0
O C:HOH741 2.1 60.3 1.0
O2B C:ADP601 2.1 57.8 1.0
O C:HOH736 2.2 66.1 1.0
OD2 C:ASP87 2.2 52.5 1.0
OD1 C:ASP87 2.3 67.7 1.0
O1A C:ADP601 2.4 43.7 1.0
CG C:ASP87 2.6 58.0 1.0
PB C:ADP601 3.4 58.6 1.0
O C:HOH743 3.7 57.0 0.9
PA C:ADP601 3.7 48.9 1.0
O3B C:ADP601 3.7 57.8 1.0
O3A C:ADP601 4.0 66.1 1.0
CB C:ASP87 4.1 49.2 1.0
C5' C:ADP601 4.2 64.2 1.0
O5' C:ADP601 4.5 64.6 1.0
O C:HOH737 4.5 62.2 1.0
N C:GLY88 4.6 43.3 1.0
O C:HOH721 4.7 42.8 0.6
O1B C:ADP601 4.7 49.3 1.0
O C:HOH752 4.8 56.6 0.8
O C:SER151 4.9 77.5 1.0
OD1 C:ASN153 4.9 88.3 1.0
O C:HOH750 4.9 51.0 1.0
CA C:SER151 4.9 55.1 1.0
CA C:ASP87 5.0 51.4 1.0

Magnesium binding site 4 out of 7 in 4ki8

Go back to Magnesium Binding Sites List in 4ki8
Magnesium binding site 4 out of 7 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State


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 A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg602

b:30.2
occ:1.00
 O D:HOH709 2.1 42.6 1.0
O D:HOH756 2.1 73.6 1.0
O D:HOH738 2.1 61.0 1.0
OD2 D:ASP87 2.1 60.6 1.0
OD1 D:ASP87 2.3 52.8 1.0
O2B D:ADP601 2.4 50.7 1.0
CG D:ASP87 2.5 53.4 1.0
O2A D:ADP601 2.6 36.1 1.0
PB D:ADP601 3.6 59.5 1.0
O3B D:ADP601 3.9 59.1 1.0
O D:HOH757 3.9 51.7 1.0
PA D:ADP601 3.9 54.7 1.0
CB D:ASP87 4.1 38.7 1.0
O3A D:ADP601 4.3 80.7 1.0
O D:ILE150 4.4 79.3 1.0
C5' D:ADP601 4.4 57.2 1.0
O D:HOH765 4.5 69.8 1.0
O D:HOH737 4.5 63.0 1.0
O D:HOH768 4.7 66.3 1.0
N D:GLY88 4.7 38.5 1.0
CA D:SER151 4.7 61.6 1.0
O D:HOH751 4.7 48.8 0.9
O D:SER151 4.7 83.0 1.0
O5' D:ADP601 4.8 42.2 1.0
O1B D:ADP601 4.9 52.6 1.0
C D:SER151 4.9 78.5 1.0
CB D:ASN153 4.9 0.6 1.0
CA D:ASP87 4.9 37.4 1.0

Magnesium binding site 5 out of 7 in 4ki8

Go back to Magnesium Binding Sites List in 4ki8
Magnesium binding site 5 out of 7 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State


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 A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg602

b:38.1
occ:1.00
 OD1 E:ASP87 2.0 83.8 1.0
O E:HOH731 2.1 83.3 1.0
O E:HOH738 2.1 70.2 1.0
O E:HOH737 2.1 93.4 1.0
O1B E:ADP601 2.1 79.1 1.0
O2A E:ADP601 2.3 64.2 1.0
CG E:ASP87 2.6 74.1 1.0
OD2 E:ASP87 3.0 85.6 1.0
O E:HOH747 3.3 80.6 1.0
PB E:ADP601 3.5 67.2 1.0
PA E:ADP601 3.7 57.8 1.0
CB E:ASP87 3.7 59.2 1.0
O3A E:ADP601 4.0 0.6 1.0
O2B E:ADP601 4.0 72.6 1.0
C5' E:ADP601 4.3 70.5 1.0
O5' E:ADP601 4.5 68.8 1.0
CA E:ASP87 4.5 60.4 1.0
O E:SER151 4.5 81.5 1.0
O3B E:ADP601 4.6 57.3 1.0
N E:GLY88 4.7 53.1 1.0
CA E:SER151 4.8 72.6 1.0
O1A E:ADP601 4.9 60.0 1.0

Magnesium binding site 6 out of 7 in 4ki8

Go back to Magnesium Binding Sites List in 4ki8
Magnesium binding site 6 out of 7 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State


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 A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg602

b:28.2
occ:1.00
 O F:HOH706 2.0 49.3 0.9
O F:HOH723 2.1 55.6 1.0
O2B F:ADP601 2.1 41.6 1.0
O F:HOH707 2.1 66.9 1.0
OD2 F:ASP87 2.2 58.2 1.0
OD1 F:ASP87 2.3 57.7 1.0
O2A F:ADP601 2.3 38.1 1.0
CG F:ASP87 2.6 50.9 1.0
PB F:ADP601 3.2 55.0 1.0
PA F:ADP601 3.5 51.5 1.0
O3B F:ADP601 3.5 64.9 1.0
O3A F:ADP601 3.7 74.4 1.0
OD1 F:ASN153 3.8 0.7 1.0
O5' F:ADP601 4.0 74.4 1.0
O F:HOH754 4.0 51.1 1.0
C5' F:ADP601 4.0 60.5 1.0
CB F:ASP87 4.1 49.4 1.0
O F:HOH744 4.3 55.6 1.0
O F:SER151 4.5 71.3 1.0
O F:HOH760 4.5 61.0 0.9
O1B F:ADP601 4.5 51.6 1.0
N F:GLY88 4.6 38.8 1.0
O F:HOH737 4.7 37.3 0.7
O F:ILE150 4.8 52.2 1.0
O F:HOH765 4.9 72.2 0.9
O1A F:ADP601 4.9 51.6 1.0
O F:HOH721 4.9 64.0 1.0
CA F:SER151 4.9 56.8 1.0
CG F:ASN153 4.9 0.6 1.0
CA F:ASP87 5.0 41.5 1.0

Magnesium binding site 7 out of 7 in 4ki8

Go back to Magnesium Binding Sites List in 4ki8
Magnesium binding site 7 out of 7 in the Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State


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 A Groel-Adp Complex in the Relaxed Allosteric State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg602

b:25.8
occ:1.00
 O G:HOH733 2.1 54.2 1.0
O G:HOH729 2.1 46.6 1.0
O G:HOH706 2.1 41.3 1.0
OD2 G:ASP87 2.2 52.5 1.0
OD1 G:ASP87 2.2 47.0 1.0
O2B G:ADP601 2.3 45.0 1.0
O2A G:ADP601 2.4 42.2 1.0
CG G:ASP87 2.5 47.9 1.0
PB G:ADP601 3.5 50.6 1.0
O3B G:ADP601 3.7 56.6 1.0
PA G:ADP601 3.7 47.5 1.0
O G:HOH779 3.9 71.5 1.0
O G:HOH712 3.9 63.5 1.0
CB G:ASP87 4.1 32.4 1.0
O3A G:ADP601 4.1 94.7 1.0
C5' G:ADP601 4.2 59.0 1.0
O G:HOH773 4.3 79.7 1.0
O G:HOH710 4.4 44.4 0.9
O5' G:ADP601 4.5 60.0 1.0
O G:HOH743 4.5 79.2 1.0
N G:GLY88 4.6 43.5 1.0
O G:ILE150 4.6 69.3 1.0
O G:SER151 4.7 76.2 1.0
O1B G:ADP601 4.8 46.7 1.0
O G:HOH784 4.9 70.8 0.9
CA G:ASP87 4.9 35.1 1.0
CA G:SER151 4.9 67.8 1.0
O1A G:ADP601 5.0 64.1 1.0

Reference:

X.Fei, D.Yang, N.Laronde-Leblanc, G.H.Lorimer. Crystal Structure of A Groel-Adp Complex in the Relaxed Allosteric State at 2.7 A Resolution. Proc.Natl.Acad.Sci.Usa V. 110 E2958 2013.
ISSN: ISSN 0027-8424
PubMed: 23861496
DOI: 10.1073/PNAS.1311996110
Page generated: Sat Aug 17 03:39:41 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy