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Sodium in PDB 2qv6: Gtp Cyclohydrolase III From M. Jannaschii (MJ0145) Complexed with Gtp and Metal Ions

Enzymatic activity of Gtp Cyclohydrolase III From M. Jannaschii (MJ0145) Complexed with Gtp and Metal Ions

All present enzymatic activity of Gtp Cyclohydrolase III From M. Jannaschii (MJ0145) Complexed with Gtp and Metal Ions:
3.5.4.29;

Protein crystallography data

The structure of Gtp Cyclohydrolase III From M. Jannaschii (MJ0145) Complexed with Gtp and Metal Ions, PDB code: 2qv6 was solved by S.A.Roberts, V.Bandarian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.31 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.203, 129.578, 90.876, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 24.4

Other elements in 2qv6:

The structure of Gtp Cyclohydrolase III From M. Jannaschii (MJ0145) Complexed with Gtp and Metal Ions also contains other interesting chemical elements:

Potassium (K) 4 atoms
Calcium (Ca) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Gtp Cyclohydrolase III From M. Jannaschii (MJ0145) Complexed with Gtp and Metal Ions (pdb code 2qv6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Gtp Cyclohydrolase III From M. Jannaschii (MJ0145) Complexed with Gtp and Metal Ions, PDB code: 2qv6:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2qv6

Go back to Sodium Binding Sites List in 2qv6
Sodium binding site 1 out of 4 in the Gtp Cyclohydrolase III From M. Jannaschii (MJ0145) Complexed with Gtp and Metal Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Gtp Cyclohydrolase III From M. Jannaschii (MJ0145) Complexed with Gtp and Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:21.0
occ:1.00
 OD1 A:ASN184 2.2 24.5 1.0
OD1 A:ASP183 2.3 22.5 1.0
O2A A:GTP300 2.3 28.9 1.0
OD1 A:ASP138 2.4 33.2 1.0
O4' A:GTP300 2.5 23.8 1.0
O A:HOH332 2.7 26.1 1.0
CG A:ASP183 3.2 23.1 1.0
CG A:ASN184 3.3 23.0 1.0
CA A:CA302 3.4 20.3 1.0
PA A:GTP300 3.5 26.2 1.0
C8 A:GTP300 3.5 23.3 1.0
C1' A:GTP300 3.5 22.8 1.0
OD2 A:ASP183 3.5 23.7 1.0
CG A:ASP138 3.6 28.3 1.0
N9 A:GTP300 3.6 23.6 1.0
C4' A:GTP300 3.6 24.8 1.0
O5' A:GTP300 3.6 24.4 1.0
C5' A:GTP300 3.7 25.7 1.0
ND2 A:ASN184 3.7 20.3 1.0
OD2 A:ASP138 4.3 27.3 1.0
N A:ASP183 4.3 23.0 1.0
N7 A:GTP300 4.3 23.6 1.0
O1A A:GTP300 4.3 22.9 1.0
C4 A:GTP300 4.4 23.0 1.0
C A:ASP183 4.5 23.0 1.0
NH2 A:ARG237 4.5 49.0 1.0
CB A:ASP183 4.5 21.6 1.0
CB A:ASP138 4.5 27.0 1.0
CB A:ASN184 4.6 22.9 1.0
O A:ASP183 4.6 24.5 1.0
O A:HOH338 4.7 32.0 1.0
CA A:ASP183 4.7 22.4 1.0
N A:ASN184 4.7 23.4 1.0
O3A A:GTP300 4.7 26.7 1.0
O1B A:GTP300 4.7 16.1 1.0
C3' A:GTP300 4.8 22.8 1.0
C5 A:GTP300 4.8 21.2 1.0
C2' A:GTP300 4.8 23.7 1.0
O3G A:GTP300 4.9 18.1 0.8
CA A:ASN184 5.0 23.0 1.0

Sodium binding site 2 out of 4 in 2qv6

Go back to Sodium Binding Sites List in 2qv6
Sodium binding site 2 out of 4 in the Gtp Cyclohydrolase III From M. Jannaschii (MJ0145) Complexed with Gtp and Metal Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Gtp Cyclohydrolase III From M. Jannaschii (MJ0145) Complexed with Gtp and Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:31.1
occ:1.00
 OD1 B:ASN184 2.1 23.2 1.0
OD1 B:ASP183 2.2 27.8 1.0
O B:HOH344 2.2 32.4 1.0
OD1 B:ASP138 2.3 35.8 1.0
O2A B:GTP300 2.4 30.7 1.0
O4' B:GTP300 2.5 26.8 1.0
CG B:ASN184 3.1 26.4 1.0
CG B:ASP183 3.1 29.6 1.0
C1' B:GTP300 3.4 25.1 1.0
ND2 B:ASN184 3.5 18.6 1.0
CG B:ASP138 3.5 30.4 1.0
OD2 B:ASP183 3.5 32.2 1.0
N9 B:GTP300 3.5 23.2 1.0
CA B:CA302 3.5 25.6 1.0
C4' B:GTP300 3.5 26.5 1.0
C8 B:GTP300 3.6 25.2 1.0
PA B:GTP300 3.7 29.4 1.0
C5' B:GTP300 3.8 26.6 1.0
O5' B:GTP300 4.0 28.6 1.0
OD2 B:ASP138 4.1 25.8 1.0
N B:ASP183 4.2 27.8 1.0
C B:ASP183 4.2 26.9 1.0
C4 B:GTP300 4.3 24.4 1.0
CB B:ASP183 4.4 27.4 1.0
CB B:ASN184 4.4 26.1 1.0
O B:ASP183 4.4 27.0 1.0
CA B:ASP183 4.5 27.7 1.0
N B:ASN184 4.5 27.2 1.0
N7 B:GTP300 4.5 22.5 1.0
O1A B:GTP300 4.5 27.4 1.0
CB B:ASP138 4.6 31.4 1.0
NH2 B:ARG237 4.6 50.8 1.0
C3' B:GTP300 4.7 24.9 1.0
C2' B:GTP300 4.7 25.2 1.0
O B:HOH345 4.7 40.2 1.0
CA B:ASN184 4.8 26.2 1.0
O1B B:GTP300 4.8 30.0 1.0
O3A B:GTP300 4.8 31.8 1.0
C5 B:GTP300 4.9 22.7 1.0

Sodium binding site 3 out of 4 in 2qv6

Go back to Sodium Binding Sites List in 2qv6
Sodium binding site 3 out of 4 in the Gtp Cyclohydrolase III From M. Jannaschii (MJ0145) Complexed with Gtp and Metal Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Gtp Cyclohydrolase III From M. Jannaschii (MJ0145) Complexed with Gtp and Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na303

b:24.0
occ:1.00
 OD1 C:ASP183 2.2 21.8 1.0
OD1 C:ASN184 2.3 21.0 1.0
OD1 C:ASP138 2.4 26.5 1.0
O4' C:GTP300 2.5 23.2 1.0
O2A C:GTP300 2.5 28.1 1.0
O C:HOH355 2.5 35.1 1.0
CG C:ASP183 3.1 23.8 1.0
CG C:ASN184 3.2 23.8 1.0
ND2 C:ASN184 3.4 17.4 1.0
C1' C:GTP300 3.5 22.4 1.0
C4' C:GTP300 3.5 23.8 1.0
OD2 C:ASP183 3.5 26.0 1.0
CA C:CA302 3.5 18.5 1.0
CG C:ASP138 3.6 26.2 1.0
N9 C:GTP300 3.6 24.2 1.0
C8 C:GTP300 3.6 23.5 1.0
C5' C:GTP300 3.6 24.9 1.0
PA C:GTP300 3.6 26.7 1.0
O5' C:GTP300 3.8 24.1 1.0
N C:ASP183 4.2 24.2 1.0
C C:ASP183 4.3 23.0 1.0
CB C:ASP183 4.3 23.5 1.0
OD2 C:ASP138 4.4 22.9 1.0
C4 C:GTP300 4.5 24.9 1.0
CA C:ASP183 4.5 23.5 1.0
N C:ASN184 4.5 23.2 1.0
N7 C:GTP300 4.5 23.3 1.0
CB C:ASN184 4.5 23.2 1.0
O1A C:GTP300 4.5 22.1 1.0
CB C:ASP138 4.5 25.3 1.0
O C:ASP183 4.6 22.7 1.0
NH2 C:ARG237 4.6 35.8 1.0
O C:HOH329 4.7 32.6 1.0
C3' C:GTP300 4.7 20.9 1.0
C2' C:GTP300 4.7 22.8 1.0
O3A C:GTP300 4.8 23.7 1.0
CA C:ASN184 4.9 23.3 1.0
C5 C:GTP300 4.9 23.6 1.0
O1B C:GTP300 4.9 17.5 1.0

Sodium binding site 4 out of 4 in 2qv6

Go back to Sodium Binding Sites List in 2qv6
Sodium binding site 4 out of 4 in the Gtp Cyclohydrolase III From M. Jannaschii (MJ0145) Complexed with Gtp and Metal Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Gtp Cyclohydrolase III From M. Jannaschii (MJ0145) Complexed with Gtp and Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na303

b:21.3
occ:1.00
 OD1 D:ASP183 2.2 25.6 1.0
OD1 D:ASN184 2.3 21.9 1.0
O2A D:GTP300 2.4 24.0 1.0
O D:HOH343 2.4 37.8 1.0
OD1 D:ASP138 2.4 22.0 1.0
O4' D:GTP300 2.5 20.5 1.0
CG D:ASP183 3.1 21.9 1.0
CG D:ASN184 3.4 22.3 1.0
CA D:CA302 3.4 21.6 1.0
OD2 D:ASP183 3.5 23.8 1.0
PA D:GTP300 3.5 24.9 1.0
C4' D:GTP300 3.5 25.6 1.0
C1' D:GTP300 3.5 20.9 1.0
C5' D:GTP300 3.5 25.7 1.0
C8 D:GTP300 3.6 20.8 1.0
N9 D:GTP300 3.6 19.4 1.0
O5' D:GTP300 3.6 26.2 1.0
CG D:ASP138 3.7 24.1 1.0
ND2 D:ASN184 3.8 21.2 1.0
N D:ASP183 4.4 20.8 1.0
NH2 D:ARG237 4.5 29.0 1.0
OD2 D:ASP138 4.5 24.8 1.0
CB D:ASP183 4.5 20.1 1.0
C D:ASP183 4.5 19.7 1.0
N7 D:GTP300 4.5 23.8 1.0
C4 D:GTP300 4.5 23.3 1.0
O1A D:GTP300 4.5 23.8 1.0
O D:ASP183 4.5 20.2 1.0
O3A D:GTP300 4.6 22.9 1.0
CB D:ASP138 4.6 24.1 1.0
CB D:ASN184 4.6 21.7 1.0
O1B D:GTP300 4.7 20.2 1.0
C3' D:GTP300 4.7 23.6 1.0
CA D:ASP183 4.7 20.5 1.0
C2' D:GTP300 4.8 21.9 1.0
N D:ASN184 4.8 20.9 1.0
O D:HOH320 4.8 34.9 1.0
C5 D:GTP300 4.9 19.2 1.0

Reference:

S.D.Morrison, S.A.Roberts, A.M.Zegeer, W.R.Montfort, V.Bandarian. A New Use For A Familiar Fold: the X-Ray Crystal Structure of Gtp-Bound Gtp Cyclohydrolase III From Methanocaldococcus Jannaschii Reveals A Two Metal Ion Catalytic Mechanism Biochemistry V. 47 230 2008.
ISSN: ISSN 0006-2960
PubMed: 18052207
DOI: 10.1021/BI701782E
Page generated: Mon Oct 7 04:04:28 2024

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