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Zinc in PDB 2p2l: RAC1-Gdp-Zinc Complex

Protein crystallography data

The structure of RAC1-Gdp-Zinc Complex, PDB code: 2p2l was solved by G.Prehna, C.E.Stebbins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.62 / 1.90
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 89.727, 89.727, 190.618, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / 20.8

Zinc Binding Sites:

The binding sites of Zinc atom in the RAC1-Gdp-Zinc Complex (pdb code 2p2l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the RAC1-Gdp-Zinc Complex, PDB code: 2p2l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2p2l

Go back to Zinc Binding Sites List in 2p2l
Zinc binding site 1 out of 8 in the RAC1-Gdp-Zinc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of RAC1-Gdp-Zinc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:26.3
occ:1.00
 O3B A:GDP200 2.1 15.6 1.0
O A:HOH1114 2.1 15.9 1.0
O A:HOH1148 2.1 18.8 1.0
OG1 A:THR17 2.2 25.2 1.0
O A:HOH915 2.2 16.4 1.0
O A:THR35 2.3 26.3 1.0
CB A:THR17 3.2 24.9 1.0
PB A:GDP200 3.3 17.9 1.0
C A:THR35 3.3 26.4 1.0
O1B A:GDP200 3.5 19.4 1.0
N A:THR17 4.0 25.7 1.0
OD2 A:ASP57 4.0 28.1 1.0
O A:PRO34 4.0 24.6 1.0
O2A A:GDP200 4.1 18.4 1.0
CA A:THR35 4.1 25.8 1.0
CA A:THR17 4.2 25.3 1.0
CG2 A:THR17 4.3 25.5 1.0
OD1 A:ASP57 4.3 28.1 1.0
N A:VAL36 4.3 26.2 1.0
O A:HOH1083 4.3 35.5 1.0
O3A A:GDP200 4.4 17.8 1.0
O2B A:GDP200 4.4 15.8 1.0
PA A:GDP200 4.5 18.4 1.0
O A:HOH905 4.5 21.1 1.0
O A:HOH1149 4.5 37.5 1.0
O A:THR58 4.5 31.7 1.0
CG A:ASP57 4.5 28.6 1.0
CA A:VAL36 4.6 26.0 1.0
O1A A:GDP200 4.7 19.9 1.0
C A:PRO34 4.9 25.7 1.0
NZ A:LYS16 4.9 24.1 1.0
O A:HOH965 4.9 27.3 1.0

Zinc binding site 2 out of 8 in 2p2l

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Zinc binding site 2 out of 8 in the RAC1-Gdp-Zinc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of RAC1-Gdp-Zinc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:28.5
occ:1.00
 OD2 A:ASP63 2.0 25.7 1.0
NE2 A:HIS104 2.0 25.9 1.0
OE2 A:GLU100 2.1 26.2 1.0
CG A:ASP63 2.6 25.3 1.0
OD1 A:ASP63 2.7 21.9 1.0
CD A:GLU100 2.8 28.6 1.0
OE1 A:GLU100 2.9 29.6 1.0
CD2 A:HIS104 3.0 25.9 1.0
CE1 A:HIS104 3.0 24.6 1.0
CB A:ASP63 4.1 25.5 1.0
ND1 A:HIS104 4.1 23.8 1.0
CG A:HIS104 4.1 24.7 1.0
NE2 A:GLN61 4.2 29.0 1.0
CG A:GLU100 4.3 26.6 1.0
N A:ASP63 4.3 26.3 1.0
CB A:GLU62 4.6 27.1 1.0
CD2 A:HIS103 4.6 19.6 1.0
CG A:GLN61 4.6 31.9 1.0
CA A:GLU100 4.6 26.9 1.0
CB A:GLU100 4.7 27.1 1.0
CA A:ASP63 4.7 26.1 1.0
O A:HOH968 4.8 27.3 1.0
O A:HOH923 4.8 28.8 1.0
CB A:HIS103 4.9 23.8 1.0
CD A:GLN61 4.9 34.0 1.0
CG A:GLU62 4.9 27.3 1.0
O A:GLU100 5.0 26.8 1.0
CG A:HIS103 5.0 21.2 1.0

Zinc binding site 3 out of 8 in 2p2l

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Zinc binding site 3 out of 8 in the RAC1-Gdp-Zinc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of RAC1-Gdp-Zinc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:28.1
occ:1.00
 OD1 A:ASP38 2.0 23.8 1.0
O A:HOH1125 2.0 19.5 1.0
OD1 B:ASP38 2.0 23.9 1.0
OD1 C:ASP38 2.0 26.1 1.0
CG A:ASP38 2.7 24.9 1.0
CG C:ASP38 2.7 24.8 1.0
OD2 A:ASP38 2.7 24.9 1.0
CG B:ASP38 2.7 21.6 1.0
OD2 C:ASP38 2.7 28.0 1.0
OD2 B:ASP38 2.8 24.9 1.0
O A:HOH1156 3.2 46.0 1.0
O A:HOH989 3.9 26.3 1.0
O B:HOH231 3.9 25.5 1.0
O C:HOH273 4.0 26.4 1.0
CB A:ASP38 4.2 26.0 1.0
CB B:ASP38 4.2 24.1 1.0
CB C:ASP38 4.2 25.3 1.0
O C:HOH207 4.3 19.0 1.0
O B:HOH234 4.3 22.0 1.0
O C:HOH219 4.3 25.7 1.0
O A:HOH1173 4.6 38.9 1.0
O B:HOH251 4.7 36.6 1.0
O B:HOH216 4.7 23.7 1.0
O C:HOH246 4.7 29.0 1.0
O C:HOH264 4.8 40.9 1.0
O A:HOH959 4.8 26.6 1.0

Zinc binding site 4 out of 8 in 2p2l

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Zinc binding site 4 out of 8 in the RAC1-Gdp-Zinc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of RAC1-Gdp-Zinc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:49.1
occ:1.00
 OE2 A:GLU131 2.0 32.0 1.0
OE1 A:GLU127 2.1 32.7 1.0
CD A:GLU131 2.9 32.0 1.0
CD A:GLU127 3.1 31.6 1.0
CG A:GLU131 3.1 32.0 1.0
CG A:GLU127 3.3 29.1 1.0
O A:HOH1136 4.0 55.8 1.0
OE1 A:GLU131 4.1 32.4 1.0
OE2 A:GLU127 4.2 33.8 1.0
NZ A:LYS130 4.3 39.4 1.0
O A:GLU127 4.6 28.5 1.0
CB A:GLU131 4.7 31.4 1.0
CB A:GLU127 4.8 29.3 1.0

Zinc binding site 5 out of 8 in 2p2l

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Zinc binding site 5 out of 8 in the RAC1-Gdp-Zinc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of RAC1-Gdp-Zinc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:28.6
occ:1.00
 O B:HOH431 2.1 17.3 1.0
O B:HOH421 2.1 18.3 1.0
OG1 B:THR17 2.2 26.4 1.0
O3B B:GDP200 2.2 19.6 1.0
O B:HOH412 2.2 19.9 1.0
O B:THR35 2.3 27.9 1.0
CB B:THR17 3.2 26.6 1.0
PB B:GDP200 3.3 20.0 1.0
C B:THR35 3.3 27.8 1.0
O1B B:GDP200 3.5 20.4 1.0
OD2 B:ASP57 3.9 29.1 1.0
N B:THR17 4.0 26.5 1.0
O B:PRO34 4.0 27.0 1.0
CA B:THR35 4.1 27.3 1.0
O2A B:GDP200 4.1 20.4 1.0
CA B:THR17 4.1 26.5 1.0
CG2 B:THR17 4.2 26.2 1.0
OD1 B:ASP57 4.3 29.5 1.0
N B:VAL36 4.3 27.2 1.0
O3A B:GDP200 4.3 20.4 1.0
O2B B:GDP200 4.4 19.4 1.0
O B:HOH327 4.4 34.0 1.0
PA B:GDP200 4.5 21.8 1.0
CG B:ASP57 4.5 29.3 1.0
O B:THR58 4.5 32.3 1.0
CA B:VAL36 4.6 27.6 1.0
O B:HOH205 4.6 23.3 1.0
O B:HOH339 4.7 42.7 1.0
O1A B:GDP200 4.8 22.4 1.0
NZ B:LYS16 4.9 24.4 1.0
C B:PRO34 4.9 27.7 1.0
CB B:LYS16 5.0 27.6 1.0

Zinc binding site 6 out of 8 in 2p2l

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Zinc binding site 6 out of 8 in the RAC1-Gdp-Zinc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of RAC1-Gdp-Zinc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:30.6
occ:1.00
 OD2 B:ASP63 2.0 25.9 1.0
NE2 B:HIS104 2.0 23.5 1.0
OE2 B:GLU100 2.1 27.1 1.0
CG B:ASP63 2.7 25.0 1.0
OD1 B:ASP63 2.8 22.6 1.0
CD B:GLU100 2.8 28.3 1.0
CD2 B:HIS104 2.9 26.6 1.0
OE1 B:GLU100 2.9 30.1 1.0
CE1 B:HIS104 3.0 26.6 1.0
CG B:HIS104 4.1 25.7 1.0
ND1 B:HIS104 4.1 25.0 1.0
CB B:ASP63 4.1 26.5 1.0
NE2 B:GLN61 4.2 28.1 1.0
CG B:GLU100 4.2 27.5 1.0
N B:ASP63 4.3 27.3 1.0
CB B:GLU62 4.5 28.8 1.0
CA B:GLU100 4.6 26.8 1.0
CB B:GLU100 4.7 26.3 1.0
CD2 B:HIS103 4.7 23.5 1.0
CG B:GLN61 4.7 32.1 1.0
CA B:ASP63 4.7 26.8 1.0
CG B:GLU62 4.9 27.4 1.0
O B:HOH305 4.9 38.6 1.0
CB B:HIS103 4.9 24.6 1.0
CD B:GLN61 4.9 33.4 1.0
O B:GLU100 4.9 26.5 1.0

Zinc binding site 7 out of 8 in 2p2l

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Zinc binding site 7 out of 8 in the RAC1-Gdp-Zinc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of RAC1-Gdp-Zinc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:26.9
occ:1.00
 O3B C:GDP200 2.1 18.9 1.0
O C:HOH443 2.1 15.9 1.0
O C:HOH434 2.1 17.3 1.0
OG1 C:THR17 2.2 25.2 1.0
O C:HOH424 2.2 19.3 1.0
O C:THR35 2.2 25.4 1.0
CB C:THR17 3.2 26.7 1.0
PB C:GDP200 3.3 19.3 1.0
C C:THR35 3.3 26.5 1.0
O1B C:GDP200 3.4 19.9 1.0
N C:THR17 4.0 25.4 1.0
OD2 C:ASP57 4.0 26.0 1.0
O C:PRO34 4.0 26.3 1.0
CA C:THR35 4.0 26.2 1.0
O2A C:GDP200 4.1 19.0 1.0
CA C:THR17 4.1 25.8 1.0
CG2 C:THR17 4.2 25.3 1.0
OD1 C:ASP57 4.3 26.4 1.0
N C:VAL36 4.3 26.5 1.0
O3A C:GDP200 4.3 19.7 1.0
O2B C:GDP200 4.3 18.8 1.0
O B:HOH420 4.4 35.0 1.0
PA C:GDP200 4.5 19.2 1.0
O B:HOH330 4.5 33.7 1.0
O C:HOH211 4.5 22.3 1.0
CG C:ASP57 4.6 28.2 1.0
O C:THR58 4.6 30.0 1.0
CA C:VAL36 4.6 26.1 1.0
O1A C:GDP200 4.7 17.9 1.0
NZ C:LYS16 4.8 24.7 1.0
C C:PRO34 4.9 26.3 1.0
CB C:LYS16 5.0 25.2 1.0
O C:HOH209 5.0 25.1 1.0

Zinc binding site 8 out of 8 in 2p2l

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Zinc binding site 8 out of 8 in the RAC1-Gdp-Zinc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of RAC1-Gdp-Zinc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:31.6
occ:1.00
 OD2 C:ASP63 2.0 23.8 1.0
NE2 C:HIS104 2.0 25.4 1.0
OE2 C:GLU100 2.1 27.5 1.0
CG C:ASP63 2.6 24.6 1.0
OD1 C:ASP63 2.7 23.9 1.0
CD C:GLU100 2.8 27.3 1.0
OE1 C:GLU100 2.9 30.1 1.0
CD2 C:HIS104 2.9 26.3 1.0
CE1 C:HIS104 3.0 27.1 1.0
ND1 C:HIS104 4.1 26.6 1.0
CG C:HIS104 4.1 25.9 1.0
CB C:ASP63 4.1 25.6 1.0
NE2 C:GLN61 4.3 29.9 1.0
CG C:GLU100 4.3 28.1 1.0
N C:ASP63 4.3 26.3 1.0
CB C:GLU62 4.5 25.4 1.0
CD2 C:HIS103 4.6 23.4 1.0
CA C:GLU100 4.6 26.7 1.0
O C:HOH253 4.7 28.2 1.0
CA C:ASP63 4.7 26.7 1.0
CG C:GLN61 4.8 30.6 1.0
CB C:GLU100 4.8 27.0 1.0
CB C:HIS103 4.9 23.1 1.0
O C:HOH263 4.9 31.8 1.0
O C:GLU100 5.0 25.6 1.0
CG C:HIS103 5.0 21.7 1.0
O C:HOH389 5.0 36.0 1.0

Reference:

G.Prehna, C.E.Stebbins. A RAC1-Gdp Trimer Complex Binds Zinc with Tetrahedral and Octahedral Coordination, Displacing Magnesium. Acta Crystallogr.,Sect.D V. 63 628 2007.
ISSN: ISSN 0907-4449
PubMed: 17452788
DOI: 10.1107/S0907444907010888
Page generated: Thu Oct 17 02:55:30 2024

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