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Magnesium in PDB 2afi: Crystal Structure of Mgadp Bound AV2-AV1 Complex

Enzymatic activity of Crystal Structure of Mgadp Bound AV2-AV1 Complex

All present enzymatic activity of Crystal Structure of Mgadp Bound AV2-AV1 Complex:
1.18.6.1;

Protein crystallography data

The structure of Crystal Structure of Mgadp Bound AV2-AV1 Complex, PDB code: 2afi was solved by F.A.Tezcan, J.T.Kaiser, D.Mustafi, M.Y.Walton, J.B.Howard, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.43 / 3.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 72.915, 141.432, 165.549, 73.69, 79.37, 76.58
R / Rfree (%) 22.9 / 27

Other elements in 2afi:

The structure of Crystal Structure of Mgadp Bound AV2-AV1 Complex also contains other interesting chemical elements:

Molybdenum (Mo) 4 atoms
Iron (Fe) 76 atoms
Calcium (Ca) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mgadp Bound AV2-AV1 Complex (pdb code 2afi). 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 Mgadp Bound AV2-AV1 Complex, PDB code: 2afi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2afi

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Magnesium binding site 1 out of 8 in the Crystal Structure of Mgadp Bound AV2-AV1 Complex


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 Mgadp Bound AV2-AV1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1291

b:44.3
occ:1.00
 OD2 E:ASP39 2.1 86.5 0.0
CG E:ASP39 2.7 86.8 0.0
OG E:SER16 2.8 77.5 1.0
O3B E:ADP1292 3.1 64.6 1.0
CB E:ASP39 3.3 87.4 0.0
OD1 E:ASP39 3.4 86.5 0.0
OD2 E:ASP43 3.6 0.2 1.0
OD1 E:ASP43 3.9 0.4 1.0
CB E:LYS41 3.9 85.3 0.0
OD2 E:ASP125 3.9 81.3 1.0
O2B E:ADP1292 4.1 61.1 1.0
CG E:ASP43 4.1 0.5 1.0
OG E:SER44 4.1 84.9 1.0
OD1 E:ASP125 4.2 83.6 1.0
PB E:ADP1292 4.2 63.4 1.0
CB E:SER16 4.2 79.1 1.0
CD E:LYS41 4.3 84.7 0.0
CG E:ASP125 4.4 81.9 1.0
CG E:LYS41 4.7 85.0 0.0
CE E:LYS15 4.7 62.4 1.0
CA E:ASP39 4.8 87.4 1.0
N E:SER16 4.9 76.9 1.0
CA E:SER16 5.0 77.2 1.0

Magnesium binding site 2 out of 8 in 2afi

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Magnesium binding site 2 out of 8 in the Crystal Structure of Mgadp Bound AV2-AV1 Complex


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 Mgadp Bound AV2-AV1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2291

b:23.0
occ:1.00
 OG F:SER16 2.2 71.2 1.0
O3B F:ADP2292 2.5 91.4 1.0
CB F:SER16 2.9 70.7 1.0
O2B F:ADP2292 2.9 93.9 1.0
PB F:ADP2292 3.2 92.4 1.0
OD2 F:ASP43 3.4 93.2 1.0
OD1 F:ASP43 3.6 93.1 1.0
O2A F:ADP2292 3.6 71.7 1.0
CG F:ASP43 3.9 90.7 1.0
OG F:SER44 3.9 83.1 1.0
O3A F:ADP2292 3.9 83.5 1.0
N F:SER16 4.0 67.7 1.0
CA F:SER16 4.0 68.6 1.0
OD1 F:ASP125 4.0 73.9 1.0
PA F:ADP2292 4.1 73.4 1.0
OD2 F:ASP39 4.3 75.8 1.0
O1A F:ADP2292 4.3 75.0 1.0
NZ F:LYS41 4.4 49.7 1.0
O1B F:ADP2292 4.6 91.1 1.0
OD2 F:ASP125 4.7 73.2 1.0
CG F:ASP39 4.7 76.2 1.0
CG F:ASP125 4.8 72.6 1.0
CB F:LYS41 4.9 69.0 1.0
N F:SER44 4.9 82.1 1.0
CB F:SER44 5.0 82.9 1.0
CA F:SER44 5.0 82.5 1.0

Magnesium binding site 3 out of 8 in 2afi

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Magnesium binding site 3 out of 8 in the Crystal Structure of Mgadp Bound AV2-AV1 Complex


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 Mgadp Bound AV2-AV1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg3291

b:41.5
occ:1.00
 O2B G:ADP3292 2.4 56.8 1.0
OD2 G:ASP39 2.8 63.8 1.0
PB G:ADP3292 3.3 50.9 1.0
O1B G:ADP3292 3.3 53.9 1.0
OG G:SER16 3.4 40.1 1.0
CG G:ASP39 3.5 62.1 1.0
OD1 G:ASP43 3.7 79.5 1.0
OD1 G:ASP125 3.7 68.7 1.0
CB G:SER16 3.9 44.0 1.0
O3B G:ADP3292 4.2 56.1 1.0
CB G:ASP39 4.2 60.2 1.0
OD1 G:ASP39 4.2 62.4 1.0
CG G:LYS41 4.2 66.2 0.0
CB G:LYS41 4.2 64.8 0.0
O1A G:ADP3292 4.4 52.6 1.0
OD2 G:ASP125 4.4 66.7 1.0
CG G:ASP125 4.5 63.7 1.0
O3A G:ADP3292 4.5 53.2 1.0
CD G:LYS41 4.6 67.2 0.0
CG G:ASP43 4.7 74.8 1.0
N G:SER16 4.7 48.4 1.0
CE G:LYS15 4.8 58.1 0.0
OD2 G:ASP43 4.9 76.9 1.0
PA G:ADP3292 4.9 54.7 1.0
CA G:SER16 4.9 45.5 1.0
NZ G:LYS15 4.9 58.7 0.0

Magnesium binding site 4 out of 8 in 2afi

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Magnesium binding site 4 out of 8 in the Crystal Structure of Mgadp Bound AV2-AV1 Complex


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 Mgadp Bound AV2-AV1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg4291

b:68.8
occ:1.00
 OD1 H:ASP43 2.0 90.5 0.0
OD2 H:ASP43 2.1 90.5 0.0
CG H:ASP43 2.4 90.0 0.0
OG H:SER16 2.6 93.7 1.0
CB H:SER16 3.2 90.4 1.0
O3A H:ADP4292 3.2 0.6 1.0
O1B H:ADP4292 3.3 0.5 1.0
CB H:ASP43 3.9 89.4 0.0
PB H:ADP4292 3.9 0.8 1.0
O2A H:ADP4292 4.1 0.9 1.0
OD2 H:ASP39 4.2 75.8 0.0
PA H:ADP4292 4.2 0.6 1.0
N H:SER44 4.3 88.2 0.0
C H:ASP43 4.3 88.5 0.0
CD H:LYS41 4.3 82.5 0.0
O2B H:ADP4292 4.4 0.3 1.0
CA H:ASP43 4.5 88.6 0.0
N H:ASP43 4.6 88.0 0.0
CA H:SER16 4.6 88.3 1.0
NZ H:LYS41 4.6 82.7 0.0
CB H:LYS41 4.6 81.8 0.0
OG H:SER44 4.6 87.9 0.0
OD1 H:ASP125 4.7 71.1 1.0
O5' H:ADP4292 4.7 0.5 1.0
O H:ASP43 4.7 88.6 0.0
CA H:SER44 4.7 87.8 0.0
CE H:LYS41 4.8 82.6 0.0
N H:SER16 4.9 88.7 1.0
CG H:ASP39 4.9 75.6 0.0

Magnesium binding site 5 out of 8 in 2afi

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Magnesium binding site 5 out of 8 in the Crystal Structure of Mgadp Bound AV2-AV1 Complex


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 Mgadp Bound AV2-AV1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg5291

b:47.3
occ:1.00
 O2B M:ADP5292 2.1 80.3 1.0
OG M:SER16 2.3 80.9 1.0
OD2 M:ASP43 2.7 85.0 0.0
CB M:SER16 3.1 80.8 1.0
CG M:ASP43 3.4 84.4 0.0
PB M:ADP5292 3.5 85.1 1.0
OD1 M:ASP43 3.5 85.0 0.0
CG M:ASP39 4.0 78.0 0.0
OG M:SER44 4.1 76.6 1.0
O3B M:ADP5292 4.1 84.3 1.0
OD2 M:ASP39 4.1 78.7 0.0
O1B M:ADP5292 4.2 85.3 1.0
OD1 M:ASP125 4.2 79.3 1.0
O1A M:ADP5292 4.2 82.7 1.0
CA M:SER16 4.3 79.2 1.0
CB M:ASP39 4.3 77.3 0.0
OD1 M:ASP39 4.3 78.6 0.0
N M:SER16 4.3 77.7 1.0
CD M:LYS41 4.5 85.3 0.0
CB M:LYS41 4.5 84.7 0.0
N M:SER44 4.5 79.5 1.0
O3A M:ADP5292 4.6 83.1 1.0
C M:ASP43 4.6 81.5 1.0
CA M:SER44 4.7 77.0 1.0
O M:ASP43 4.8 83.4 1.0
CB M:ASP43 4.8 83.9 0.0
CB M:SER44 5.0 77.2 1.0
CG M:LYS41 5.0 85.0 0.0

Magnesium binding site 6 out of 8 in 2afi

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Magnesium binding site 6 out of 8 in the Crystal Structure of Mgadp Bound AV2-AV1 Complex


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 Mgadp Bound AV2-AV1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg6291

b:46.7
occ:1.00
 OD2 N:ASP43 2.0 0.4 1.0
CD N:LYS41 2.0 0.6 0.0
CE N:LYS41 2.4 0.3 0.0
CG N:ASP43 2.6 0.5 1.0
NZ N:LYS41 2.7 100.0 0.0
CB N:LYS41 2.7 0.9 0.0
OD1 N:ASP43 2.8 0.8 1.0
O2B N:ADP6292 2.8 0.2 1.0
CG N:LYS41 2.8 0.2 0.0
O1B N:ADP6292 3.7 0.9 1.0
PB N:ADP6292 3.7 0.4 1.0
O3A N:ADP6292 3.8 0.1 1.0
CB N:ASP43 4.1 0.0 1.0
CA N:LYS41 4.2 0.2 1.0
OG N:SER16 4.5 94.9 1.0
C N:LYS41 4.6 0.5 1.0
N N:ASP43 4.7 0.7 1.0
O N:LYS41 4.9 1.0 1.0

Magnesium binding site 7 out of 8 in 2afi

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Magnesium binding site 7 out of 8 in the Crystal Structure of Mgadp Bound AV2-AV1 Complex


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 Mgadp Bound AV2-AV1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg7291

b:39.6
occ:1.00
 OG O:SER16 2.0 65.6 1.0
O1B O:ADP7292 2.1 69.0 1.0
CB O:SER16 3.0 64.4 1.0
O1A O:ADP7292 3.2 71.7 1.0
OD2 O:ASP43 3.3 92.0 1.0
PB O:ADP7292 3.5 73.5 1.0
OD2 O:ASP39 3.9 85.2 1.0
O3A O:ADP7292 4.0 72.0 1.0
CG O:ASP43 4.0 88.2 1.0
OD1 O:ASP43 4.1 89.0 1.0
O3B O:ADP7292 4.1 69.5 1.0
CG O:ASP39 4.1 80.1 1.0
PA O:ADP7292 4.1 68.7 1.0
CA O:SER16 4.2 63.5 1.0
OG O:SER44 4.3 74.6 1.0
OD1 O:ASP125 4.3 79.6 1.0
N O:SER16 4.3 65.3 1.0
OD1 O:ASP39 4.4 79.9 1.0
OD2 O:ASP125 4.6 75.2 1.0
CB O:ASP39 4.6 76.1 1.0
O2A O:ADP7292 4.7 66.2 1.0
N O:SER44 4.7 75.4 1.0
O2B O:ADP7292 4.7 69.9 1.0
CA O:SER44 4.7 74.4 1.0
CG O:ASP125 4.8 78.4 1.0
CB O:SER44 4.8 74.3 1.0
CB O:LYS41 4.9 75.2 1.0
C O:ASP43 5.0 77.7 1.0
CD O:LYS41 5.0 79.0 1.0

Magnesium binding site 8 out of 8 in 2afi

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Magnesium binding site 8 out of 8 in the Crystal Structure of Mgadp Bound AV2-AV1 Complex


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 Mgadp Bound AV2-AV1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg8291

b:66.5
occ:1.00
 O3B P:ADP8292 2.6 0.3 1.0
OD2 P:ASP43 2.7 91.4 0.0
OG P:SER16 2.9 90.4 1.0
OD1 P:ASP43 2.9 91.4 0.0
CG P:ASP43 3.1 91.1 0.0
CB P:SER16 3.1 87.8 1.0
O2B P:ADP8292 3.4 0.3 1.0
PB P:ADP8292 3.4 0.8 1.0
OD1 P:ASP125 3.7 95.8 1.0
O3A P:ADP8292 3.8 0.6 1.0
OD2 P:ASP125 4.0 94.0 1.0
CG P:ASP39 4.1 0.7 1.0
CG P:ASP125 4.2 93.6 1.0
OD2 P:ASP39 4.2 0.6 1.0
N P:SER44 4.3 89.0 0.0
CA P:SER16 4.3 86.1 1.0
CB P:ASP39 4.4 0.1 1.0
OD1 P:ASP39 4.4 0.2 1.0
CB P:SER44 4.4 88.3 0.0
N P:SER16 4.4 85.8 1.0
OG P:SER44 4.5 88.2 0.0
CA P:SER44 4.5 88.2 0.0
CB P:LYS41 4.5 90.6 0.0
CB P:ASP43 4.5 90.7 0.0
C P:ASP43 4.6 89.7 0.0
N P:ASP43 4.7 90.4 0.0
O1B P:ADP8292 4.8 0.1 1.0
O1A P:ADP8292 5.0 0.6 1.0
CA P:ASP43 5.0 90.2 0.0
CD P:LYS41 5.0 89.4 0.0

Reference:

F.A.Tezcan, J.T.Kaiser, D.Mustafi, M.Y.Walton, J.B.Howard, D.C.Rees. Nitrogenase Complexes: Multiple Docking Sites For A Nucleotide Switch Protein Science V. 309 1377 2005.
ISSN: ISSN 0036-8075
PubMed: 16123301
DOI: 10.1126/SCIENCE.1115653
Page generated: Tue Aug 13 21:28:56 2024

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